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1298 lines
54 KiB
1298 lines
54 KiB
1 molecule converted |
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Welcome to antechamber 21.0: molecular input file processor. |
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The atom type is set to gaff; the options available to the -at flag are |
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gaff, gaff2, amber, bcc, and sybyl. |
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Info: Determining atomic numbers from atomic symbols which are case sensitive. |
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Running: /home/adit/miniconda3/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac |
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/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash) |
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Running: /home/adit/miniconda3/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff |
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/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash) |
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Info: Total number of electrons: 32; net charge: 0 |
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Running: /home/adit/miniconda3/bin/sqm -O -i sqm.in -o sqm.out |
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Running: /home/adit/miniconda3/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /home/adit/miniconda3/dat/antechamber/BCCPARM.DAT -s 2 -j 1 |
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/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash) |
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Running: /home/adit/miniconda3/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC |
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/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash) |
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-I: Adding /home/adit/miniconda3/dat/leap/prep to search path. |
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-I: Adding /home/adit/miniconda3/dat/leap/lib to search path. |
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-I: Adding /home/adit/miniconda3/dat/leap/parm to search path. |
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-I: Adding /home/adit/miniconda3/dat/leap/cmd to search path. |
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-f: Source tleap.in. |
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Welcome to LEaP! |
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(no leaprc in search path) |
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Sourcing: ./tleap.in |
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----- Source: /home/adit/miniconda3/dat/leap/cmd/leaprc.gaff |
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----- Source of /home/adit/miniconda3/dat/leap/cmd/leaprc.gaff done |
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Log file: ./leap.log |
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Loading parameters: /home/adit/miniconda3/dat/leap/parm/gaff.dat |
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Reading title: |
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AMBER General Force Field for organic molecules (Version 1.81, May 2017) |
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Loading Mol2 file: ./urea_mod.mol2 |
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Reading MOLECULE named URA |
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Loading parameters: ./urea.frcmod |
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Reading force field modification type file (frcmod) |
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Reading title: |
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Remark line goes here |
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Checking 'URA'.... |
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Checking parameters for unit 'URA'. |
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Checking for bond parameters. |
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Checking for angle parameters. |
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Unit is OK. |
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Building topology. |
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Building atom parameters. |
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Checking Unit. |
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Building topology. |
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Building atom parameters. |
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Building bond parameters. |
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Building angle parameters. |
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Building proper torsion parameters. |
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Building improper torsion parameters. |
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total 3 improper torsions applied |
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Building H-Bond parameters. |
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Incorporating Non-Bonded adjustments. |
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Not Marking per-residue atom chain types. |
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Marking per-residue atom chain types. |
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(Residues lacking connect0/connect1 - |
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these don't have chain types marked: |
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res total affected |
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URA 1 |
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) |
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(no restraints) |
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Writing pdb file: URA_gaff.pdb |
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Quit |
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Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0. |
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1 molecule converted |
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Welcome to antechamber 21.0: molecular input file processor. |
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The atom type is set to gaff; the options available to the -at flag are |
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gaff, gaff2, amber, bcc, and sybyl. |
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Info: Determining atomic numbers from atomic symbols which are case sensitive. |
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Running: /home/adit/miniconda3/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac |
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/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash) |
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Running: /home/adit/miniconda3/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff |
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/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash) |
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Info: Total number of electrons: 10; net charge: 0 |
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Running: /home/adit/miniconda3/bin/sqm -O -i sqm.in -o sqm.out |
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Running: /home/adit/miniconda3/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /home/adit/miniconda3/dat/antechamber/BCCPARM.DAT -s 2 -j 1 |
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/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash) |
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Running: /home/adit/miniconda3/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC |
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/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash) |
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-I: Adding /home/adit/miniconda3/dat/leap/prep to search path. |
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-I: Adding /home/adit/miniconda3/dat/leap/lib to search path. |
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-I: Adding /home/adit/miniconda3/dat/leap/parm to search path. |
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-I: Adding /home/adit/miniconda3/dat/leap/cmd to search path. |
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-f: Source tleap.in. |
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Welcome to LEaP! |
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(no leaprc in search path) |
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Sourcing: ./tleap.in |
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----- Source: /home/adit/miniconda3/dat/leap/cmd/leaprc.gaff |
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----- Source of /home/adit/miniconda3/dat/leap/cmd/leaprc.gaff done |
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Log file: ./leap.log |
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Loading parameters: /home/adit/miniconda3/dat/leap/parm/gaff.dat |
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Reading title: |
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AMBER General Force Field for organic molecules (Version 1.81, May 2017) |
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Loading Mol2 file: ./amoniak_mod.mol2 |
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Reading MOLECULE named AMK |
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Loading parameters: ./amoniak.frcmod |
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Reading force field modification type file (frcmod) |
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Reading title: |
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Remark line goes here |
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Checking 'AMK'.... |
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Checking parameters for unit 'AMK'. |
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Checking for bond parameters. |
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Checking for angle parameters. |
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Unit is OK. |
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Building topology. |
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Building atom parameters. |
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Checking Unit. |
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Building topology. |
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Building atom parameters. |
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Building bond parameters. |
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Building angle parameters. |
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Building proper torsion parameters. |
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Building improper torsion parameters. |
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total 0 improper torsions applied |
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Building H-Bond parameters. |
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Incorporating Non-Bonded adjustments. |
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Not Marking per-residue atom chain types. |
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Marking per-residue atom chain types. |
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(Residues lacking connect0/connect1 - |
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these don't have chain types marked: |
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res total affected |
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AMK 1 |
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) |
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(no restraints) |
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Writing pdb file: AMK_gaff.pdb |
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Quit |
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Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0. |
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1 molecule converted |
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Welcome to antechamber 21.0: molecular input file processor. |
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The atom type is set to gaff; the options available to the -at flag are |
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gaff, gaff2, amber, bcc, and sybyl. |
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Info: Determining atomic numbers from atomic symbols which are case sensitive. |
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Running: /home/adit/miniconda3/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac |
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/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash) |
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Running: /home/adit/miniconda3/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff |
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/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash) |
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Info: Total number of electrons: 10; net charge: 0 |
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Running: /home/adit/miniconda3/bin/sqm -O -i sqm.in -o sqm.out |
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Running: /home/adit/miniconda3/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /home/adit/miniconda3/dat/antechamber/BCCPARM.DAT -s 2 -j 1 |
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/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash) |
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Running: /home/adit/miniconda3/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC |
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/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash) |
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-I: Adding /home/adit/miniconda3/dat/leap/prep to search path. |
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-I: Adding /home/adit/miniconda3/dat/leap/lib to search path. |
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-I: Adding /home/adit/miniconda3/dat/leap/parm to search path. |
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-I: Adding /home/adit/miniconda3/dat/leap/cmd to search path. |
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-f: Source tleap.in. |
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Welcome to LEaP! |
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(no leaprc in search path) |
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Sourcing: ./tleap.in |
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----- Source: /home/adit/miniconda3/dat/leap/cmd/leaprc.gaff |
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----- Source of /home/adit/miniconda3/dat/leap/cmd/leaprc.gaff done |
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Log file: ./leap.log |
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Loading parameters: /home/adit/miniconda3/dat/leap/parm/gaff.dat |
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Reading title: |
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AMBER General Force Field for organic molecules (Version 1.81, May 2017) |
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Loading Mol2 file: ./air_mod.mol2 |
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Reading MOLECULE named SLV |
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Loading parameters: ./air.frcmod |
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Reading force field modification type file (frcmod) |
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Reading title: |
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Remark line goes here |
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Checking 'SLV'.... |
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Checking parameters for unit 'SLV'. |
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Checking for bond parameters. |
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Checking for angle parameters. |
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Unit is OK. |
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Building topology. |
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Building atom parameters. |
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Checking Unit. |
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Building topology. |
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Building atom parameters. |
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Building bond parameters. |
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Building angle parameters. |
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Building proper torsion parameters. |
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Building improper torsion parameters. |
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total 0 improper torsions applied |
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Building H-Bond parameters. |
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Incorporating Non-Bonded adjustments. |
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Not Marking per-residue atom chain types. |
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Marking per-residue atom chain types. |
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(Residues lacking connect0/connect1 - |
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these don't have chain types marked: |
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res total affected |
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SLV 1 |
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) |
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(no restraints) |
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Writing pdb file: air_gaff.pdb |
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Quit |
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Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0. |
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################################################################################ |
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PACKMOL - Packing optimization for the automated generation of |
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starting configurations for molecular dynamics simulations. |
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Version 20.3.5 |
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################################################################################ |
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Packmol must be run with: packmol < inputfile.inp |
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Userguide at: http://m3g.iqm.unicamp.br/packmol |
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Reading input file... (Control-C aborts) |
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Seed for random number generator: 1234567 |
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Output file: system_init.pdb |
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Reading coordinate file: ../air/air_gaff.pdb |
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Reading coordinate file: ../urea/URA_gaff.pdb |
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Reading coordinate file: ../amoniak/AMK_gaff.pdb |
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Number of independent structures: 3 |
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The structures are: |
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Structure 1 :../air/air_gaff.pdb( 3 atoms) |
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Structure 2 :../urea/URA_gaff.pdb( 8 atoms) |
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Structure 3 :../amoniak/AMK_gaff.pdb( 4 atoms) |
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Maximum number of GENCAN loops for all molecule packing: 600 |
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Total number of restrictions: 3 |
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Distance tolerance: 2.5000000000000000 |
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Residue numbering set for structure 1 : 3 |
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Swap chains of molecules of structure 1 : F |
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Residue numbering set for structure 2 : 3 |
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Swap chains of molecules of structure 2 : F |
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Residue numbering set for structure 3 : 3 |
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Swap chains of molecules of structure 3 : F |
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Number of molecules of type 1 : 100 |
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Number of molecules of type 2 : 4 |
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Number of molecules of type 3 : 6 |
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Total number of atoms: 356 |
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Total number of molecules: 110 |
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Number of fixed molecules: 0 |
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Number of free molecules: 110 |
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Number of variables: 660 |
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Total number of fixed atoms: 0 |
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Maximum internal distance of type 1 : 1.5652360844294384 |
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Maximum internal distance of type 2 : 4.1398118314725361 |
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Maximum internal distance of type 3 : 1.6920218674709850 |
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All atoms must be within these coordinates: |
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x: [ -1000.0000000000000 , 1000.0000000000000 ] |
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y: [ -1000.0000000000000 , 1000.0000000000000 ] |
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z: [ -1000.0000000000000 , 1000.0000000000000 ] |
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If the system is larger than this, increase the sidemax parameter. |
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################################################################################ |
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Building initial approximation ... |
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################################################################################ |
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Adjusting initial point to fit the constraints |
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-------------------------------------------------------------------------------- |
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-------------------------------------------------------------------------------- |
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Molecules of type: 1 |
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Packing:|0 100%| |
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|********************* |
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Restraint-only function value: 3.1232090093930659E-002 |
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Maximum violation of the restraints: 6.6657659524056671E-003 |
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-------------------------------------------------------------------------------- |
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Molecules of type: 2 |
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Packing:|0 100%| |
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|**************************** |
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Restraint-only function value: 0.0000000000000000 |
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Maximum violation of the restraints: 0.0000000000000000 |
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-------------------------------------------------------------------------------- |
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Molecules of type: 3 |
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Packing:|0 100%| |
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|*********************************** |
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Restraint-only function value: 0.0000000000000000 |
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Maximum violation of the restraints: 0.0000000000000000 |
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-------------------------------------------------------------------------------- |
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Rescaling maximum and minimum coordinates... |
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Computing size of patches... |
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Add fixed molecules to permanent arrays... |
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Reseting center of mass... |
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-------------------------------------------------------------------------------- |
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Setting initial trial coordinates ... |
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-------------------------------------------------------------------------------- |
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-------------------------------------------------------------------------------- |
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Molecules of type: 1 |
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Adjusting random positions to fit the constraints. |
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Packing:|0 100%| |
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|************** |
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Restraint-only function value: 8.3612852464226903E-007 |
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Maximum violation of the restraints: 8.2959702213215425E-007 |
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-------------------------------------------------------------------------------- |
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Molecules of type: 2 |
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Adjusting random positions to fit the constraints. |
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Restraint-only function value: 0.0000000000000000 |
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Maximum violation of the restraints: 0.0000000000000000 |
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-------------------------------------------------------------------------------- |
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Molecules of type: 3 |
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Adjusting random positions to fit the constraints. |
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Restraint-only function value: 4.7701008096379498E-003 |
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Maximum violation of the restraints: 4.7701008096379498E-003 |
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################################################################################ |
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Objective function at initial point: 11209.106817311276 |
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################################################################################ |
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Packing molecules of type: 1 |
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################################################################################ |
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-------------------------------------------------------------------------------- |
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Starting GENCAN loop: 0 |
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Scaling radii by: 1.1000000000000001 |
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Packing:|0 100%| |
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|******************************************************************| |
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|******************************************************************| |
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Function value from last GENCAN loop: f = .22510E+00 |
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Best function value before: f = .67065E+04 |
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Improvement from best function value: 99.99 % |
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Improvement from last loop: 99.99 % |
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Maximum violation of target distance: 0.000000 |
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Maximum violation of the constraints: .52389E-01 |
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All-type function value: .32678E+04 |
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-------------------------------------------------------------------------------- |
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-------------------------------------------------------------------------------- |
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Starting GENCAN loop: 1 |
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Scaling radii by: 1.1000000000000001 |
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Packing:|0 100%| |
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|************************************************* |
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Function value from last GENCAN loop: f = .26447E-01 |
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Best function value before: f = .22510E+00 |
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Improvement from best function value: 88.25 % |
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Improvement from last loop: 88.25 % |
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Maximum violation of target distance: 0.000000 |
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Maximum violation of the constraints: .82462E-02 |
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Current structure written to file: system_init.pdb |
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-------------------------------------------------------------------------------- |
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Packing solved for molecules of type 1 |
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Objective function value: 2.6446755000934657E-002 |
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Maximum violation of target distance: 0.0000000000000000 |
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Max. constraint violation: 8.2462179949114763E-003 |
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-------------------------------------------------------------------------------- |
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################################################################################ |
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Packing molecules of type: 2 |
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################################################################################ |
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-------------------------------------------------------------------------------- |
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Starting GENCAN loop: 0 |
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Scaling radii by: 1.1000000000000001 |
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Packing:|0 100%| |
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|******* |
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Function value from last GENCAN loop: f = .00000E+00 |
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Best function value before: f = .19336E+03 |
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Improvement from best function value: 99.99 % |
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Improvement from last loop: 99.99 % |
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Maximum violation of target distance: 0.000000 |
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Maximum violation of the constraints: .00000E+00 |
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Current structure written to file: system_init.pdb |
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-------------------------------------------------------------------------------- |
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Packing solved for molecules of type 2 |
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Objective function value: 0.0000000000000000 |
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Maximum violation of target distance: 0.0000000000000000 |
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Max. constraint violation: 0.0000000000000000 |
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-------------------------------------------------------------------------------- |
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################################################################################ |
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Packing molecules of type: 3 |
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################################################################################ |
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-------------------------------------------------------------------------------- |
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Starting GENCAN loop: 0 |
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Scaling radii by: 1.1000000000000001 |
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Packing:|0 100%| |
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|************** |
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Function value from last GENCAN loop: f = .00000E+00 |
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Best function value before: f = .18699E+03 |
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Improvement from best function value: 99.99 % |
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Improvement from last loop: 99.99 % |
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Maximum violation of target distance: 0.000000 |
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Maximum violation of the constraints: .00000E+00 |
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Current structure written to file: system_init.pdb |
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-------------------------------------------------------------------------------- |
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Packing solved for molecules of type 3 |
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Objective function value: 0.0000000000000000 |
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Maximum violation of target distance: 0.0000000000000000 |
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Max. constraint violation: 0.0000000000000000 |
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-------------------------------------------------------------------------------- |
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################################################################################ |
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Packing all molecules together |
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################################################################################ |
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-------------------------------------------------------------------------------- |
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Starting GENCAN loop: 0 |
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Scaling radii by: 1.1000000000000001 |
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Packing:|0 100%| |
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|******************************************************************| |
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|******************************************************************| |
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Function value from last GENCAN loop: f = .17935E+01 |
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Best function value before: f = .25506E+04 |
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Improvement from best function value: 99.93 % |
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Improvement from last loop: 99.93 % |
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Maximum violation of target distance: 0.000000 |
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Maximum violation of the constraints: .24107E+00 |
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-------------------------------------------------------------------------------- |
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-------------------------------------------------------------------------------- |
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Starting GENCAN loop: 1 |
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Scaling radii by: 1.1000000000000001 |
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Packing:|0 100%| |
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|******************************************************************| |
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|******************************************************************| |
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Function value from last GENCAN loop: f = .89791E-01 |
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Best function value before: f = .17935E+01 |
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Improvement from best function value: 94.99 % |
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Improvement from last loop: 94.99 % |
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Maximum violation of target distance: 0.000000 |
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Maximum violation of the constraints: .27350E-01 |
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-------------------------------------------------------------------------------- |
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-------------------------------------------------------------------------------- |
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Starting GENCAN loop: 2 |
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Scaling radii by: 1.1000000000000001 |
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Packing:|0 100%| |
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|****************************************** |
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Function value from last GENCAN loop: f = .28746E-01 |
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Best function value before: f = .89791E-01 |
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Improvement from best function value: 67.99 % |
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Improvement from last loop: 67.99 % |
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Maximum violation of target distance: 0.000000 |
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Maximum violation of the constraints: .89654E-02 |
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################################################################################ |
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Success! |
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Final objective function value: .28746E-01 |
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Maximum violation of target distance: 0.000000 |
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Maximum violation of the constraints: .89654E-02 |
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-------------------------------------------------------------------------------- |
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Please cite this work if Packmol was useful: |
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L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez, |
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PACKMOL: A package for building initial configurations for |
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molecular dynamics simulations. |
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Journal of Computational Chemistry, 30:2157-2164,2009. |
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################################################################################ |
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Solution written to file: system_init.pdb |
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-------------------------------------------------------------------------------- |
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Running time: 0.223801002 seconds. |
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-------------------------------------------------------------------------------- |
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-I: Adding /home/adit/miniconda3/dat/leap/prep to search path. |
|
-I: Adding /home/adit/miniconda3/dat/leap/lib to search path. |
|
-I: Adding /home/adit/miniconda3/dat/leap/parm to search path. |
|
-I: Adding /home/adit/miniconda3/dat/leap/cmd to search path. |
|
-f: Source tleap.in. |
|
|
|
Welcome to LEaP! |
|
(no leaprc in search path) |
|
Sourcing: ./tleap.in |
|
----- Source: /home/adit/miniconda3/dat/leap/cmd/leaprc.gaff |
|
----- Source of /home/adit/miniconda3/dat/leap/cmd/leaprc.gaff done |
|
Log file: ./leap.log |
|
Loading parameters: /home/adit/miniconda3/dat/leap/parm/gaff.dat |
|
Reading title: |
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017) |
|
Loading parameters: /home/adit/miniconda3/dat/leap/parm/frcmod.ions1lm_iod |
|
Reading force field modification type file (frcmod) |
|
Reading title: |
|
Li/Merz ion parameters of monovalent ions for TIP3P, SPC/E and TIP4P/EW water models (12-6 IOD set) |
|
Loading library: ../urea/URA.lib |
|
Loading parameters: ../urea/urea.frcmod |
|
Reading force field modification type file (frcmod) |
|
Reading title: |
|
Remark line goes here |
|
Loading library: ../amoniak/AMK.lib |
|
Loading parameters: ../amoniak/amoniak.frcmod |
|
Reading force field modification type file (frcmod) |
|
Reading title: |
|
Remark line goes here |
|
Loading library: ../air/air.lib |
|
Loading parameters: ../air/air.frcmod |
|
Reading force field modification type file (frcmod) |
|
Reading title: |
|
Remark line goes here |
|
Loading PDB file: ./system_init.pdb |
|
(starting new molecule for chain B) |
|
(starting new molecule for chain C) |
|
total atoms in file: 356 |
|
AMK SLV SYSTEM URA gaff |
|
Checking Unit. |
|
|
|
/home/adit/miniconda3/bin/teLeap: Warning! |
|
The unperturbed charge of the unit (-0.104000) is not integral. |
|
|
|
/home/adit/miniconda3/bin/teLeap: Warning! |
|
The unperturbed charge of the unit (-0.104000) is not zero. |
|
|
|
/home/adit/miniconda3/bin/teLeap: Note. |
|
Ignoring the error and warning from Unit Checking. |
|
|
|
Building topology. |
|
Building atom parameters. |
|
Building bond parameters. |
|
Building angle parameters. |
|
Building proper torsion parameters. |
|
Building improper torsion parameters. |
|
total 12 improper torsions applied |
|
Building H-Bond parameters. |
|
Incorporating Non-Bonded adjustments. |
|
Not Marking per-residue atom chain types. |
|
Marking per-residue atom chain types. |
|
(Residues lacking connect0/connect1 - |
|
these don't have chain types marked: |
|
|
|
res total affected |
|
|
|
AMK 6 |
|
SLV 100 |
|
URA 4 |
|
) |
|
(no restraints) |
|
Writing pdb file: system.pdb |
|
Quit |
|
|
|
Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. |
|
======================================================================================== |
|
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2021-02-05T22:15:50CET (c) 2022 AWSdS | |
|
======================================================================================== |
|
Converting Amber input files to Gromacs ... |
|
==> Writing GROMACS files |
|
|
|
==> Writing GMX dihedrals for GMX 4.5 and higher. |
|
|
|
Total time of execution: less than a second |
|
Note that major changes are planned in future for editconf, to improve usability and utility. |
|
Read 356 atoms |
|
No velocities found |
|
system size : 1.530 1.527 1.537 (nm) |
|
diameter : 2.530 (nm) |
|
center : -0.063 -0.010 0.009 (nm) |
|
box vectors : 0.000 0.000 0.000 (nm) |
|
box angles : 0.00 0.00 0.00 (degrees) |
|
box volume : 0.00 (nm^3) |
|
shift : 0.824 0.770 0.752 (nm) |
|
new center : 0.761 0.761 0.761 (nm) |
|
new box vectors : 1.521 1.521 1.521 (nm) |
|
new box angles : 90.00 90.00 90.00 (degrees) |
|
new box volume : 3.52 (nm^3) |
|
Ignoring obsolete mdp entry 'ns_type' |
|
|
|
NOTE 1 [file minim.mdp]: |
|
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note |
|
that with the Verlet scheme, nstlist has no effect on the accuracy of |
|
your simulation. |
|
|
|
|
|
NOTE 2 [file minim.mdp]: |
|
You have set rlist larger than the interaction cut-off, but you also have |
|
verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. |
|
|
|
Generating 1-4 interactions: fudge = 0.5 |
|
Number of degrees of freedom in T-Coupling group rest is 1065.00 |
|
|
|
There were 2 notes |
|
Setting the LD random seed to -1651968805 |
|
|
|
Generated 28 of the 28 non-bonded parameter combinations |
|
|
|
Generated 28 of the 28 1-4 parameter combinations |
|
|
|
Excluding 3 bonded neighbours molecule type 'system' |
|
Analysing residue names: |
|
There are: 110 Other residues |
|
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... |
|
Calculating fourier grid dimensions for X Y Z |
|
Using a fourier grid of 14x14x14, spacing 0.109 0.109 0.109 |
|
|
|
Estimate for the relative computational load of the PME mesh part: 0.39 |
|
|
|
This run will generate roughly 0 Mb of data |
|
Reading file mini.tpr, VERSION 2021.3 (single precision) |
|
Using 1 MPI thread |
|
Using 1 OpenMP thread |
|
|
|
|
|
NOTE: Thread affinity was not set. |
|
|
|
Steepest Descents: |
|
Tolerance (Fmax) = 1.00000e+02 |
|
Number of steps = 50000 |
|
|
|
writing lowest energy coordinates. |
|
|
|
Steepest Descents converged to Fmax < 100 in 933 steps |
|
Potential Energy = -1.9001487e+03 |
|
Maximum force = 9.8961441e+01 on atom 325 |
|
Norm of force = 2.1945789e+01 |
|
Reading file mini.tpr, VERSION 2021.3 (single precision) |
|
Reading file mini.tpr, VERSION 2021.3 (single precision) |
|
trr version: GMX_trn_file (single precision) |
|
|
|
Reading frame 0 time 933.000 |
|
Last frame 0 time 933.000 |
|
Analyzed 1 frames, last time 933.000 |
|
Ignoring obsolete mdp entry 'ns_type' |
|
|
|
NOTE 1 [file nve.mdp]: |
|
You have set rlist larger than the interaction cut-off, but you also have |
|
verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. |
|
|
|
Generating 1-4 interactions: fudge = 0.5 |
|
|
|
WARNING 1 [file system_GMX.top, line 878]: |
|
The following macros were defined in the 'define' mdp field with the -D |
|
prefix, but were not used in the topology: |
|
FLEXIBLE |
|
If you haven't made a spelling error, either use the macro you defined, |
|
or don't define the macro |
|
|
|
|
|
NOTE 2 [file system_GMX.top, line 878]: |
|
For energy conservation with LINCS, lincs_iter should be 2 or larger. |
|
|
|
|
|
Number of degrees of freedom in T-Coupling group rest is 831.00 |
|
|
|
NOTE 3 [file nve.mdp]: |
|
NVE simulation with an initial temperature of zero: will use a Verlet |
|
buffer of 10%. Check your energy drift! |
|
|
|
|
|
There were 3 notes |
|
|
|
There was 1 warning |
|
Setting the LD random seed to -170428545 |
|
|
|
Generated 28 of the 28 non-bonded parameter combinations |
|
|
|
Generated 28 of the 28 1-4 parameter combinations |
|
|
|
Excluding 3 bonded neighbours molecule type 'system' |
|
|
|
turning H bonds into constraints... |
|
Analysing residue names: |
|
There are: 110 Other residues |
|
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... |
|
Calculating fourier grid dimensions for X Y Z |
|
Using a fourier grid of 10x10x10, spacing 0.152 0.152 0.152 |
|
|
|
Estimate for the relative computational load of the PME mesh part: 0.34 |
|
|
|
This run will generate roughly 0 Mb of data |
|
Reading file nve.tpr, VERSION 2021.3 (single precision) |
|
Can not increase nstlist because an NVE ensemble is used |
|
Using 1 MPI thread |
|
Using 1 OpenMP thread |
|
|
|
|
|
NOTE: Thread affinity was not set. |
|
starting mdrun 'system' |
|
1000 steps, 1.0 ps. |
|
|
|
step 0 |
|
step 100, remaining wall clock time: 0 s |
|
step 200, remaining wall clock time: 0 s |
|
step 300, remaining wall clock time: 0 s |
|
step 400, remaining wall clock time: 0 s |
|
step 500, remaining wall clock time: 0 s |
|
step 600, remaining wall clock time: 0 s |
|
step 700, remaining wall clock time: 0 s |
|
step 800, remaining wall clock time: 0 s |
|
step 900, remaining wall clock time: 0 s |
|
Writing final coordinates. |
|
|
|
step 1000, remaining wall clock time: 0 s |
|
NOTE: 16 % of the run time was spent in pair search, |
|
you might want to increase nstlist (this has no effect on accuracy) |
|
|
|
Core t (s) Wall t (s) (%) |
|
Time: 0.276 0.276 100.0 |
|
(ns/day) (hour/ns) |
|
Performance: 312.939 0.077 |
|
Ignoring obsolete mdp entry 'ns_type' |
|
|
|
NOTE 1 [file nvt.mdp]: |
|
You have set rlist larger than the interaction cut-off, but you also have |
|
verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. |
|
|
|
Generating 1-4 interactions: fudge = 0.5 |
|
|
|
WARNING 1 [file system_GMX.top, line 878]: |
|
The following macros were defined in the 'define' mdp field with the -D |
|
prefix, but were not used in the topology: |
|
FLEXIBLE |
|
If you haven't made a spelling error, either use the macro you defined, |
|
or don't define the macro |
|
|
|
Number of degrees of freedom in T-Coupling group System is 831.00 |
|
|
|
There was 1 note |
|
|
|
There was 1 warning |
|
Setting the LD random seed to -1212318339 |
|
|
|
Generated 28 of the 28 non-bonded parameter combinations |
|
|
|
Generated 28 of the 28 1-4 parameter combinations |
|
|
|
Excluding 3 bonded neighbours molecule type 'system' |
|
|
|
turning H bonds into constraints... |
|
|
|
Setting gen_seed to -1057953 |
|
|
|
Velocities were taken from a Maxwell distribution at 298.15 K |
|
Analysing residue names: |
|
There are: 110 Other residues |
|
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... |
|
|
|
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298.15 K |
|
|
|
Calculated rlist for 1x1 atom pair-list as 0.665 nm, buffer size 0.004 nm |
|
|
|
Set rlist, assuming 4x4 atom pair-list, to 0.661 nm, buffer size 0.000 nm |
|
|
|
Note that mdrun will redetermine rlist based on the actual pair-list setup |
|
Calculating fourier grid dimensions for X Y Z |
|
Using a fourier grid of 10x10x10, spacing 0.152 0.152 0.152 |
|
|
|
Estimate for the relative computational load of the PME mesh part: 0.39 |
|
|
|
This run will generate roughly 0 Mb of data |
|
Reading file nvt.tpr, VERSION 2021.3 (single precision) |
|
Changing nstlist from 10 to 100, rlist from 0.66055 to 0.73055 |
|
|
|
Using 1 MPI thread |
|
Using 1 OpenMP thread |
|
|
|
|
|
NOTE: Thread affinity was not set. |
|
starting mdrun 'system' |
|
1000 steps, 1.0 ps. |
|
|
|
step 0 |
|
step 100, remaining wall clock time: 0 s |
|
step 200, remaining wall clock time: 0 s |
|
step 300, remaining wall clock time: 0 s |
|
step 400, remaining wall clock time: 0 s |
|
step 500, remaining wall clock time: 0 s |
|
step 600, remaining wall clock time: 0 s |
|
step 700, remaining wall clock time: 0 s |
|
step 800, remaining wall clock time: 0 s |
|
step 900, remaining wall clock time: 0 s |
|
Writing final coordinates. |
|
|
|
step 1000, remaining wall clock time: 0 s |
|
Core t (s) Wall t (s) (%) |
|
Time: 0.174 0.174 100.0 |
|
(ns/day) (hour/ns) |
|
Performance: 498.125 0.048 |
|
Ignoring obsolete mdp entry 'title' |
|
Ignoring obsolete mdp entry 'ns_type' |
|
|
|
NOTE 1 [file npt.mdp]: |
|
You have set rlist larger than the interaction cut-off, but you also have |
|
verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. |
|
|
|
Generating 1-4 interactions: fudge = 0.5 |
|
Number of degrees of freedom in T-Coupling group System is 831.00 |
|
|
|
Last frame -1 time 1.000 |
|
|
|
There was 1 note |
|
Setting the LD random seed to -843057670 |
|
|
|
Generated 28 of the 28 non-bonded parameter combinations |
|
|
|
Generated 28 of the 28 1-4 parameter combinations |
|
|
|
Excluding 3 bonded neighbours molecule type 'system' |
|
|
|
turning H bonds into constraints... |
|
Analysing residue names: |
|
There are: 110 Other residues |
|
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... |
|
|
|
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298.15 K |
|
|
|
Calculated rlist for 1x1 atom pair-list as 0.678 nm, buffer size 0.017 nm |
|
|
|
Set rlist, assuming 4x4 atom pair-list, to 0.661 nm, buffer size 0.000 nm |
|
|
|
Note that mdrun will redetermine rlist based on the actual pair-list setup |
|
|
|
Reading Coordinates, Velocities and Box size from old trajectory |
|
|
|
Will read whole trajectory |
|
|
|
Using frame at t = 1 ps |
|
|
|
Starting time for run is 0 ps |
|
Calculating fourier grid dimensions for X Y Z |
|
Using a fourier grid of 10x10x10, spacing 0.152 0.152 0.152 |
|
|
|
Estimate for the relative computational load of the PME mesh part: 0.38 |
|
|
|
This run will generate roughly 0 Mb of data |
|
Reading file npt.tpr, VERSION 2021.3 (single precision) |
|
Changing nstlist from 10 to 50, rlist from 0.66055 to 0.72955 |
|
|
|
Using 1 MPI thread |
|
Using 1 OpenMP thread |
|
|
|
|
|
NOTE: Thread affinity was not set. |
|
starting mdrun 'system' |
|
1000 steps, 2.0 ps. |
|
|
|
step 0 |
|
step 100, remaining wall clock time: 0 s |
|
step 200, remaining wall clock time: 0 s |
|
step 300, remaining wall clock time: 0 s |
|
step 400, remaining wall clock time: 0 s |
|
step 500, remaining wall clock time: 0 s |
|
step 600, remaining wall clock time: 0 s |
|
step 700, remaining wall clock time: 0 s |
|
step 800, remaining wall clock time: 0 s |
|
step 900, remaining wall clock time: 0 s |
|
Writing final coordinates. |
|
|
|
step 1000, remaining wall clock time: 0 s |
|
Core t (s) Wall t (s) (%) |
|
Time: 0.203 0.203 99.9 |
|
(ns/day) (hour/ns) |
|
Performance: 853.022 0.028 |
|
Ignoring obsolete mdp entry 'title' |
|
Ignoring obsolete mdp entry 'ns_type' |
|
|
|
NOTE 1 [file nptp.mdp]: |
|
You have set rlist larger than the interaction cut-off, but you also have |
|
verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. |
|
|
|
Generating 1-4 interactions: fudge = 0.5 |
|
Number of degrees of freedom in T-Coupling group System is 1065.00 |
|
|
|
There was 1 note |
|
Setting the LD random seed to -1715476549 |
|
|
|
Generated 28 of the 28 non-bonded parameter combinations |
|
|
|
Generated 28 of the 28 1-4 parameter combinations |
|
|
|
Excluding 3 bonded neighbours molecule type 'system' |
|
Analysing residue names: |
|
There are: 110 Other residues |
|
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... |
|
|
|
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298.15 K |
|
|
|
Calculated rlist for 1x1 atom pair-list as 0.662 nm, buffer size 0.001 nm |
|
|
|
Set rlist, assuming 4x4 atom pair-list, to 0.661 nm, buffer size 0.000 nm |
|
|
|
Note that mdrun will redetermine rlist based on the actual pair-list setup |
|
Calculating fourier grid dimensions for X Y Z |
|
Using a fourier grid of 12x12x12, spacing 0.134 0.134 0.134 |
|
|
|
Estimate for the relative computational load of the PME mesh part: 0.40 |
|
|
|
This run will generate roughly 0 Mb of data |
|
Reading file nptp.tpr, VERSION 2021.3 (single precision) |
|
Changing nstlist from 10 to 100, rlist from 0.66055 to 0.71255 |
|
|
|
Using 1 MPI thread |
|
Using 1 OpenMP thread |
|
|
|
|
|
NOTE: Thread affinity was not set. |
|
starting mdrun 'system' |
|
1000 steps, 0.5 ps. |
|
|
|
step 0 |
|
step 100, remaining wall clock time: 0 s |
|
step 200, remaining wall clock time: 0 s |
|
step 300, remaining wall clock time: 0 s |
|
step 400, remaining wall clock time: 0 s |
|
step 500, remaining wall clock time: 0 s |
|
step 600, remaining wall clock time: 0 s |
|
step 700, remaining wall clock time: 0 s |
|
step 800, remaining wall clock time: 0 s |
|
step 900, remaining wall clock time: 0 s |
|
Writing final coordinates. |
|
|
|
step 1000, remaining wall clock time: 0 s |
|
Core t (s) Wall t (s) (%) |
|
Time: 0.175 0.175 100.0 |
|
(ns/day) (hour/ns) |
|
Performance: 246.587 0.097 |
|
Will write pdb: Protein data bank file |
|
Reading file nptp.tpr, VERSION 2021.3 (single precision) |
|
Reading file nptp.tpr, VERSION 2021.3 (single precision) |
|
Group 0 ( System) has 356 elements |
|
There is one group in the index |
|
trr version: GMX_trn_file (single precision) |
|
|
|
Reading frame 0 time 0.000 -> frame 0 time 0.000 |
|
|
|
Reading frame 1 time 0.250 -> frame 1 time 0.250 |
|
|
|
Reading frame 2 time 0.500 -> frame 2 time 0.500 |
|
|
|
Last frame 2 time 0.500 |
|
|
|
Note that major changes are planned in future for trjconv, to improve usability and utility. |
|
Select group for output |
|
:-) GROMACS - gmx select, 2021.3 (-: |
|
|
|
GROMACS is written by: |
|
Andrey Alekseenko Emile Apol Rossen Apostolov |
|
Paul Bauer Herman J.C. Berendsen Par Bjelkmar |
|
Christian Blau Viacheslav Bolnykh Kevin Boyd |
|
Aldert van Buuren Rudi van Drunen Anton Feenstra |
|
Gilles Gouaillardet Alan Gray Gerrit Groenhof |
|
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang |
|
Aleksei Iupinov Christoph Junghans Joe Jordan |
|
Dimitrios Karkoulis Peter Kasson Jiri Kraus |
|
Carsten Kutzner Per Larsson Justin A. Lemkul |
|
Viveca Lindahl Magnus Lundborg Erik Marklund |
|
Pascal Merz Pieter Meulenhoff Teemu Murtola |
|
Szilard Pall Sander Pronk Roland Schulz |
|
Michael Shirts Alexey Shvetsov Alfons Sijbers |
|
Peter Tieleman Jon Vincent Teemu Virolainen |
|
Christian Wennberg Maarten Wolf Artem Zhmurov |
|
and the project leaders: |
|
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel |
|
|
|
Copyright (c) 1991-2000, University of Groningen, The Netherlands. |
|
Copyright (c) 2001-2019, The GROMACS development team at |
|
Uppsala University, Stockholm University and |
|
the Royal Institute of Technology, Sweden. |
|
check out http://www.gromacs.org for more information. |
|
|
|
GROMACS is free software; you can redistribute it and/or modify it |
|
under the terms of the GNU Lesser General Public License |
|
as published by the Free Software Foundation; either version 2.1 |
|
of the License, or (at your option) any later version. |
|
|
|
GROMACS: gmx select, version 2021.3 |
|
Executable: /usr/local/gromacs/bin/gmx |
|
Data prefix: /usr/local/gromacs |
|
Working dir: /home/adit/MySoftware/CMMDE/examples/larutan/UreaAirAmonia/SistemLarutan |
|
Command line: |
|
gmx select -f nptp.gro -s nptp.tpr -on SLV.ndx -select '(resname SLV)' |
|
|
|
Reading file nptp.tpr, VERSION 2021.3 (single precision) |
|
Reading file nptp.tpr, VERSION 2021.3 (single precision) |
|
Reading frames from gro file 'system', 356 atoms. |
|
|
|
Reading frame 0 time 0.000 |
|
Last frame 0 time 0.000 |
|
Analyzed 1 frames, last time 0.000 |
|
|
|
GROMACS reminds you: "It's Not Dark Yet, But It's Getting There" (Bob Dylan) |
|
|
|
:-) GROMACS - gmx msd, 2021.3 (-: |
|
|
|
GROMACS is written by: |
|
Andrey Alekseenko Emile Apol Rossen Apostolov |
|
Paul Bauer Herman J.C. Berendsen Par Bjelkmar |
|
Christian Blau Viacheslav Bolnykh Kevin Boyd |
|
Aldert van Buuren Rudi van Drunen Anton Feenstra |
|
Gilles Gouaillardet Alan Gray Gerrit Groenhof |
|
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang |
|
Aleksei Iupinov Christoph Junghans Joe Jordan |
|
Dimitrios Karkoulis Peter Kasson Jiri Kraus |
|
Carsten Kutzner Per Larsson Justin A. Lemkul |
|
Viveca Lindahl Magnus Lundborg Erik Marklund |
|
Pascal Merz Pieter Meulenhoff Teemu Murtola |
|
Szilard Pall Sander Pronk Roland Schulz |
|
Michael Shirts Alexey Shvetsov Alfons Sijbers |
|
Peter Tieleman Jon Vincent Teemu Virolainen |
|
Christian Wennberg Maarten Wolf Artem Zhmurov |
|
and the project leaders: |
|
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel |
|
|
|
Copyright (c) 1991-2000, University of Groningen, The Netherlands. |
|
Copyright (c) 2001-2019, The GROMACS development team at |
|
Uppsala University, Stockholm University and |
|
the Royal Institute of Technology, Sweden. |
|
check out http://www.gromacs.org for more information. |
|
|
|
GROMACS is free software; you can redistribute it and/or modify it |
|
under the terms of the GNU Lesser General Public License |
|
as published by the Free Software Foundation; either version 2.1 |
|
of the License, or (at your option) any later version. |
|
|
|
GROMACS: gmx msd, version 2021.3 |
|
Executable: /usr/local/gromacs/bin/gmx |
|
Data prefix: /usr/local/gromacs |
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Working dir: /home/adit/MySoftware/CMMDE/examples/larutan/UreaAirAmonia/SistemLarutan |
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Command line: |
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gmx msd -f nptp.trr -s nptp.tpr -n SLV.ndx -o msd_SLV.xvg |
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|
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Reading file nptp.tpr, VERSION 2021.3 (single precision) |
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Reading file nptp.tpr, VERSION 2021.3 (single precision) |
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|
|
Select a group to calculate mean squared displacement for: |
|
Group 0 ( (resname_SLV)) has 300 elements |
|
There is one group in the index |
|
trr version: GMX_trn_file (single precision) |
|
|
|
Reading frame 0 time 0.000 |
|
Reading frame 1 time 0.250 |
|
Reading frame 2 time 0.500 |
|
Last frame 2 time 0.500 |
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|
|
Used 1 restart points spaced 10 ps over 0.5 ps |
|
|
|
|
|
GROMACS reminds you: "It's Not Dark Yet, But It's Getting There" (Bob Dylan) |
|
|
|
Fitting from 0 to 0.5 ps |
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|
|
D[(resname_SLV)] 18.1354 (+/- 0.0000) 1e-5 cm^2/s |
|
:-) GROMACS - gmx select, 2021.3 (-: |
|
|
|
GROMACS is written by: |
|
Andrey Alekseenko Emile Apol Rossen Apostolov |
|
Paul Bauer Herman J.C. Berendsen Par Bjelkmar |
|
Christian Blau Viacheslav Bolnykh Kevin Boyd |
|
Aldert van Buuren Rudi van Drunen Anton Feenstra |
|
Gilles Gouaillardet Alan Gray Gerrit Groenhof |
|
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang |
|
Aleksei Iupinov Christoph Junghans Joe Jordan |
|
Dimitrios Karkoulis Peter Kasson Jiri Kraus |
|
Carsten Kutzner Per Larsson Justin A. Lemkul |
|
Viveca Lindahl Magnus Lundborg Erik Marklund |
|
Pascal Merz Pieter Meulenhoff Teemu Murtola |
|
Szilard Pall Sander Pronk Roland Schulz |
|
Michael Shirts Alexey Shvetsov Alfons Sijbers |
|
Peter Tieleman Jon Vincent Teemu Virolainen |
|
Christian Wennberg Maarten Wolf Artem Zhmurov |
|
and the project leaders: |
|
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel |
|
|
|
Copyright (c) 1991-2000, University of Groningen, The Netherlands. |
|
Copyright (c) 2001-2019, The GROMACS development team at |
|
Uppsala University, Stockholm University and |
|
the Royal Institute of Technology, Sweden. |
|
check out http://www.gromacs.org for more information. |
|
|
|
GROMACS is free software; you can redistribute it and/or modify it |
|
under the terms of the GNU Lesser General Public License |
|
as published by the Free Software Foundation; either version 2.1 |
|
of the License, or (at your option) any later version. |
|
|
|
GROMACS: gmx select, version 2021.3 |
|
Executable: /usr/local/gromacs/bin/gmx |
|
Data prefix: /usr/local/gromacs |
|
Working dir: /home/adit/MySoftware/CMMDE/examples/larutan/UreaAirAmonia/SistemLarutan |
|
Command line: |
|
gmx select -f nptp.gro -s nptp.tpr -on URA.ndx -select '(resname URA)' |
|
|
|
Reading file nptp.tpr, VERSION 2021.3 (single precision) |
|
Reading file nptp.tpr, VERSION 2021.3 (single precision) |
|
Reading frames from gro file 'system', 356 atoms. |
|
|
|
Reading frame 0 time 0.000 |
|
Last frame 0 time 0.000 |
|
Analyzed 1 frames, last time 0.000 |
|
|
|
GROMACS reminds you: "It's Not Dark Yet, But It's Getting There" (Bob Dylan) |
|
|
|
:-) GROMACS - gmx msd, 2021.3 (-: |
|
|
|
GROMACS is written by: |
|
Andrey Alekseenko Emile Apol Rossen Apostolov |
|
Paul Bauer Herman J.C. Berendsen Par Bjelkmar |
|
Christian Blau Viacheslav Bolnykh Kevin Boyd |
|
Aldert van Buuren Rudi van Drunen Anton Feenstra |
|
Gilles Gouaillardet Alan Gray Gerrit Groenhof |
|
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang |
|
Aleksei Iupinov Christoph Junghans Joe Jordan |
|
Dimitrios Karkoulis Peter Kasson Jiri Kraus |
|
Carsten Kutzner Per Larsson Justin A. Lemkul |
|
Viveca Lindahl Magnus Lundborg Erik Marklund |
|
Pascal Merz Pieter Meulenhoff Teemu Murtola |
|
Szilard Pall Sander Pronk Roland Schulz |
|
Michael Shirts Alexey Shvetsov Alfons Sijbers |
|
Peter Tieleman Jon Vincent Teemu Virolainen |
|
Christian Wennberg Maarten Wolf Artem Zhmurov |
|
and the project leaders: |
|
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel |
|
|
|
Copyright (c) 1991-2000, University of Groningen, The Netherlands. |
|
Copyright (c) 2001-2019, The GROMACS development team at |
|
Uppsala University, Stockholm University and |
|
the Royal Institute of Technology, Sweden. |
|
check out http://www.gromacs.org for more information. |
|
|
|
GROMACS is free software; you can redistribute it and/or modify it |
|
under the terms of the GNU Lesser General Public License |
|
as published by the Free Software Foundation; either version 2.1 |
|
of the License, or (at your option) any later version. |
|
|
|
GROMACS: gmx msd, version 2021.3 |
|
Executable: /usr/local/gromacs/bin/gmx |
|
Data prefix: /usr/local/gromacs |
|
Working dir: /home/adit/MySoftware/CMMDE/examples/larutan/UreaAirAmonia/SistemLarutan |
|
Command line: |
|
gmx msd -f nptp.trr -s nptp.tpr -n URA.ndx -o msd_URA.xvg |
|
|
|
Reading file nptp.tpr, VERSION 2021.3 (single precision) |
|
Reading file nptp.tpr, VERSION 2021.3 (single precision) |
|
|
|
Select a group to calculate mean squared displacement for: |
|
Group 0 ( (resname_URA)) has 32 elements |
|
There is one group in the index |
|
trr version: GMX_trn_file (single precision) |
|
|
|
Reading frame 0 time 0.000 |
|
Reading frame 1 time 0.250 |
|
Reading frame 2 time 0.500 |
|
Last frame 2 time 0.500 |
|
|
|
Used 1 restart points spaced 10 ps over 0.5 ps |
|
|
|
|
|
GROMACS reminds you: "It's Not Dark Yet, But It's Getting There" (Bob Dylan) |
|
|
|
Fitting from 0 to 0.5 ps |
|
|
|
D[(resname_URA)] 19.8046 (+/- 0.0000) 1e-5 cm^2/s |
|
:-) GROMACS - gmx select, 2021.3 (-: |
|
|
|
GROMACS is written by: |
|
Andrey Alekseenko Emile Apol Rossen Apostolov |
|
Paul Bauer Herman J.C. Berendsen Par Bjelkmar |
|
Christian Blau Viacheslav Bolnykh Kevin Boyd |
|
Aldert van Buuren Rudi van Drunen Anton Feenstra |
|
Gilles Gouaillardet Alan Gray Gerrit Groenhof |
|
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang |
|
Aleksei Iupinov Christoph Junghans Joe Jordan |
|
Dimitrios Karkoulis Peter Kasson Jiri Kraus |
|
Carsten Kutzner Per Larsson Justin A. Lemkul |
|
Viveca Lindahl Magnus Lundborg Erik Marklund |
|
Pascal Merz Pieter Meulenhoff Teemu Murtola |
|
Szilard Pall Sander Pronk Roland Schulz |
|
Michael Shirts Alexey Shvetsov Alfons Sijbers |
|
Peter Tieleman Jon Vincent Teemu Virolainen |
|
Christian Wennberg Maarten Wolf Artem Zhmurov |
|
and the project leaders: |
|
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel |
|
|
|
Copyright (c) 1991-2000, University of Groningen, The Netherlands. |
|
Copyright (c) 2001-2019, The GROMACS development team at |
|
Uppsala University, Stockholm University and |
|
the Royal Institute of Technology, Sweden. |
|
check out http://www.gromacs.org for more information. |
|
|
|
GROMACS is free software; you can redistribute it and/or modify it |
|
under the terms of the GNU Lesser General Public License |
|
as published by the Free Software Foundation; either version 2.1 |
|
of the License, or (at your option) any later version. |
|
|
|
GROMACS: gmx select, version 2021.3 |
|
Executable: /usr/local/gromacs/bin/gmx |
|
Data prefix: /usr/local/gromacs |
|
Working dir: /home/adit/MySoftware/CMMDE/examples/larutan/UreaAirAmonia/SistemLarutan |
|
Command line: |
|
gmx select -f nptp.gro -s nptp.tpr -on AMK.ndx -select '(resname AMK)' |
|
|
|
Reading file nptp.tpr, VERSION 2021.3 (single precision) |
|
Reading file nptp.tpr, VERSION 2021.3 (single precision) |
|
Reading frames from gro file 'system', 356 atoms. |
|
|
|
Reading frame 0 time 0.000 |
|
Last frame 0 time 0.000 |
|
Analyzed 1 frames, last time 0.000 |
|
|
|
GROMACS reminds you: "It's Not Dark Yet, But It's Getting There" (Bob Dylan) |
|
|
|
:-) GROMACS - gmx msd, 2021.3 (-: |
|
|
|
GROMACS is written by: |
|
Andrey Alekseenko Emile Apol Rossen Apostolov |
|
Paul Bauer Herman J.C. Berendsen Par Bjelkmar |
|
Christian Blau Viacheslav Bolnykh Kevin Boyd |
|
Aldert van Buuren Rudi van Drunen Anton Feenstra |
|
Gilles Gouaillardet Alan Gray Gerrit Groenhof |
|
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang |
|
Aleksei Iupinov Christoph Junghans Joe Jordan |
|
Dimitrios Karkoulis Peter Kasson Jiri Kraus |
|
Carsten Kutzner Per Larsson Justin A. Lemkul |
|
Viveca Lindahl Magnus Lundborg Erik Marklund |
|
Pascal Merz Pieter Meulenhoff Teemu Murtola |
|
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx msd, version 2021.3
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/adit/MySoftware/CMMDE/examples/larutan/UreaAirAmonia/SistemLarutan
Command line:
gmx msd -f nptp.trr -s nptp.tpr -n AMK.ndx -o msd_AMK.xvg
Reading file nptp.tpr, VERSION 2021.3 (single precision)
Reading file nptp.tpr, VERSION 2021.3 (single precision)
Select a group to calculate mean squared displacement for:
Group 0 ( (resname_AMK)) has 24 elements
There is one group in the index
trr version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Reading frame 1 time 0.250
Reading frame 2 time 0.500
Last frame 2 time 0.500
Used 1 restart points spaced 10 ps over 0.5 ps
GROMACS reminds you: "It's Not Dark Yet, But It's Getting There" (Bob Dylan)
Fitting from 0 to 0.5 ps
D[(resname_AMK)] 17.1270 (+/- 0.0000) 1e-5 cm^2/s
Suhu: 298.1500 K
0.6605496122701092
Membuat sistem larutan menggunakan PACKMOL
================================================================================
tolerance 2.5
filetype pdb
output system_init.pdb
structure ../air/air_gaff.pdb
number 100
inside cube -7.605496122701092 -7.605496122701092 -7.605496122701092 15.210992245402185
resnumbers 3
end structure
structure ../urea/URA_gaff.pdb
number 4
inside cube -7.605496122701092 -7.605496122701092 -7.605496122701092 15.210992245402185
resnumbers 3
end structure
structure ../amoniak/AMK_gaff.pdb
number 6
inside cube -7.605496122701092 -7.605496122701092 -7.605496122701092 15.210992245402185
resnumbers 3
end structure
================================================================================
Melakukan perhitungan MSD untuk pelarut
Melakukan perhitungan MSD untuk terlarut, masukkan masing-masing terlarut
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