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A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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CMMDE/examples/larutan/UreaAirAmonia/slurm-2690.out

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First launching
2 years ago
1 molecule converted
Welcome to antechamber 21.0: molecular input file processor.
The atom type is set to gaff; the options available to the -at flag are
gaff, gaff2, amber, bcc, and sybyl.
Info: Determining atomic numbers from atomic symbols which are case sensitive.
Running: /home/adit/miniconda3/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash)
Running: /home/adit/miniconda3/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash)
Info: Total number of electrons: 32; net charge: 0
Running: /home/adit/miniconda3/bin/sqm -O -i sqm.in -o sqm.out
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
/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash)
Running: /home/adit/miniconda3/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash)
-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 Mol2 file: ./urea_mod.mol2
Reading MOLECULE named URA
Loading parameters: ./urea.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Checking 'URA'....
Checking parameters for unit 'URA'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
Building topology.
Building atom parameters.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 3 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
URA 1
)
(no restraints)
Writing pdb file: URA_gaff.pdb
Quit
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
1 molecule converted
Welcome to antechamber 21.0: molecular input file processor.
The atom type is set to gaff; the options available to the -at flag are
gaff, gaff2, amber, bcc, and sybyl.
Info: Determining atomic numbers from atomic symbols which are case sensitive.
Running: /home/adit/miniconda3/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash)
Running: /home/adit/miniconda3/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash)
Info: Total number of electrons: 10; net charge: 0
Running: /home/adit/miniconda3/bin/sqm -O -i sqm.in -o sqm.out
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
/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash)
Running: /home/adit/miniconda3/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash)
-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 Mol2 file: ./amoniak_mod.mol2
Reading MOLECULE named AMK
Loading parameters: ./amoniak.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Checking 'AMK'....
Checking parameters for unit 'AMK'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
Building topology.
Building atom parameters.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 0 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 1
)
(no restraints)
Writing pdb file: AMK_gaff.pdb
Quit
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
1 molecule converted
Welcome to antechamber 21.0: molecular input file processor.
The atom type is set to gaff; the options available to the -at flag are
gaff, gaff2, amber, bcc, and sybyl.
Info: Determining atomic numbers from atomic symbols which are case sensitive.
Running: /home/adit/miniconda3/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash)
Running: /home/adit/miniconda3/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash)
Info: Total number of electrons: 10; net charge: 0
Running: /home/adit/miniconda3/bin/sqm -O -i sqm.in -o sqm.out
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
/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash)
Running: /home/adit/miniconda3/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
/bin/bash: /home/adit/miniconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash)
-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 Mol2 file: ./air_mod.mol2
Reading MOLECULE named SLV
Loading parameters: ./air.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Checking 'SLV'....
Checking parameters for unit 'SLV'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
Building topology.
Building atom parameters.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 0 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
SLV 1
)
(no restraints)
Writing pdb file: air_gaff.pdb
Quit
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
################################################################################
PACKMOL - Packing optimization for the automated generation of
starting configurations for molecular dynamics simulations.
Version 20.3.5
################################################################################
Packmol must be run with: packmol < inputfile.inp
Userguide at: http://m3g.iqm.unicamp.br/packmol
Reading input file... (Control-C aborts)
Seed for random number generator: 1234567
Output file: system_init.pdb
Reading coordinate file: ../air/air_gaff.pdb
Reading coordinate file: ../urea/URA_gaff.pdb
Reading coordinate file: ../amoniak/AMK_gaff.pdb
Number of independent structures: 3
The structures are:
Structure 1 :../air/air_gaff.pdb( 3 atoms)
Structure 2 :../urea/URA_gaff.pdb( 8 atoms)
Structure 3 :../amoniak/AMK_gaff.pdb( 4 atoms)
Maximum number of GENCAN loops for all molecule packing: 600
Total number of restrictions: 3
Distance tolerance: 2.5000000000000000
Residue numbering set for structure 1 : 3
Swap chains of molecules of structure 1 : F
Residue numbering set for structure 2 : 3
Swap chains of molecules of structure 2 : F
Residue numbering set for structure 3 : 3
Swap chains of molecules of structure 3 : F
Number of molecules of type 1 : 100
Number of molecules of type 2 : 4
Number of molecules of type 3 : 6
Total number of atoms: 356
Total number of molecules: 110
Number of fixed molecules: 0
Number of free molecules: 110
Number of variables: 660
Total number of fixed atoms: 0
Maximum internal distance of type 1 : 1.5652360844294384
Maximum internal distance of type 2 : 4.1398118314725361
Maximum internal distance of type 3 : 1.6920218674709850
All atoms must be within these coordinates:
x: [ -1000.0000000000000 , 1000.0000000000000 ]
y: [ -1000.0000000000000 , 1000.0000000000000 ]
z: [ -1000.0000000000000 , 1000.0000000000000 ]
If the system is larger than this, increase the sidemax parameter.
################################################################################
Building initial approximation ...
################################################################################
Adjusting initial point to fit the constraints
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Molecules of type: 1
Packing:|0 100%|
|*********************
Restraint-only function value: 3.1232090093930659E-002
Maximum violation of the restraints: 6.6657659524056671E-003
--------------------------------------------------------------------------------
Molecules of type: 2
Packing:|0 100%|
|****************************
Restraint-only function value: 0.0000000000000000
Maximum violation of the restraints: 0.0000000000000000
--------------------------------------------------------------------------------
Molecules of type: 3
Packing:|0 100%|
|***********************************
Restraint-only function value: 0.0000000000000000
Maximum violation of the restraints: 0.0000000000000000
--------------------------------------------------------------------------------
Rescaling maximum and minimum coordinates...
Computing size of patches...
Add fixed molecules to permanent arrays...
Reseting center of mass...
--------------------------------------------------------------------------------
Setting initial trial coordinates ...
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Molecules of type: 1
Adjusting random positions to fit the constraints.
Packing:|0 100%|
|**************
Restraint-only function value: 8.3612852464226903E-007
Maximum violation of the restraints: 8.2959702213215425E-007
--------------------------------------------------------------------------------
Molecules of type: 2
Adjusting random positions to fit the constraints.
Restraint-only function value: 0.0000000000000000
Maximum violation of the restraints: 0.0000000000000000
--------------------------------------------------------------------------------
Molecules of type: 3
Adjusting random positions to fit the constraints.
Restraint-only function value: 4.7701008096379498E-003
Maximum violation of the restraints: 4.7701008096379498E-003
################################################################################
Objective function at initial point: 11209.106817311276
################################################################################
Packing molecules of type: 1
################################################################################
--------------------------------------------------------------------------------
Starting GENCAN loop: 0
Scaling radii by: 1.1000000000000001
Packing:|0 100%|
|******************************************************************|
|******************************************************************|
Function value from last GENCAN loop: f = .22510E+00
Best function value before: f = .67065E+04
Improvement from best function value: 99.99 %
Improvement from last loop: 99.99 %
Maximum violation of target distance: 0.000000
Maximum violation of the constraints: .52389E-01
All-type function value: .32678E+04
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Starting GENCAN loop: 1
Scaling radii by: 1.1000000000000001
Packing:|0 100%|
|*************************************************
Function value from last GENCAN loop: f = .26447E-01
Best function value before: f = .22510E+00
Improvement from best function value: 88.25 %
Improvement from last loop: 88.25 %
Maximum violation of target distance: 0.000000
Maximum violation of the constraints: .82462E-02
Current structure written to file: system_init.pdb
--------------------------------------------------------------------------------
Packing solved for molecules of type 1
Objective function value: 2.6446755000934657E-002
Maximum violation of target distance: 0.0000000000000000
Max. constraint violation: 8.2462179949114763E-003
--------------------------------------------------------------------------------
################################################################################
Packing molecules of type: 2
################################################################################
--------------------------------------------------------------------------------
Starting GENCAN loop: 0
Scaling radii by: 1.1000000000000001
Packing:|0 100%|
|*******
Function value from last GENCAN loop: f = .00000E+00
Best function value before: f = .19336E+03
Improvement from best function value: 99.99 %
Improvement from last loop: 99.99 %
Maximum violation of target distance: 0.000000
Maximum violation of the constraints: .00000E+00
Current structure written to file: system_init.pdb
--------------------------------------------------------------------------------
Packing solved for molecules of type 2
Objective function value: 0.0000000000000000
Maximum violation of target distance: 0.0000000000000000
Max. constraint violation: 0.0000000000000000
--------------------------------------------------------------------------------
################################################################################
Packing molecules of type: 3
################################################################################
--------------------------------------------------------------------------------
Starting GENCAN loop: 0
Scaling radii by: 1.1000000000000001
Packing:|0 100%|
|**************
Function value from last GENCAN loop: f = .00000E+00
Best function value before: f = .18699E+03
Improvement from best function value: 99.99 %
Improvement from last loop: 99.99 %
Maximum violation of target distance: 0.000000
Maximum violation of the constraints: .00000E+00
Current structure written to file: system_init.pdb
--------------------------------------------------------------------------------
Packing solved for molecules of type 3
Objective function value: 0.0000000000000000
Maximum violation of target distance: 0.0000000000000000
Max. constraint violation: 0.0000000000000000
--------------------------------------------------------------------------------
################################################################################
Packing all molecules together
################################################################################
--------------------------------------------------------------------------------
Starting GENCAN loop: 0
Scaling radii by: 1.1000000000000001
Packing:|0 100%|
|******************************************************************|
|******************************************************************|
Function value from last GENCAN loop: f = .17935E+01
Best function value before: f = .25506E+04
Improvement from best function value: 99.93 %
Improvement from last loop: 99.93 %
Maximum violation of target distance: 0.000000
Maximum violation of the constraints: .24107E+00
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Starting GENCAN loop: 1
Scaling radii by: 1.1000000000000001
Packing:|0 100%|
|******************************************************************|
|******************************************************************|
Function value from last GENCAN loop: f = .89791E-01
Best function value before: f = .17935E+01
Improvement from best function value: 94.99 %
Improvement from last loop: 94.99 %
Maximum violation of target distance: 0.000000
Maximum violation of the constraints: .27350E-01
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Starting GENCAN loop: 2
Scaling radii by: 1.1000000000000001
Packing:|0 100%|
|******************************************
Function value from last GENCAN loop: f = .28746E-01
Best function value before: f = .89791E-01
Improvement from best function value: 67.99 %
Improvement from last loop: 67.99 %
Maximum violation of target distance: 0.000000
Maximum violation of the constraints: .89654E-02
################################################################################
Success!
Final objective function value: .28746E-01
Maximum violation of target distance: 0.000000
Maximum violation of the constraints: .89654E-02
--------------------------------------------------------------------------------
Please cite this work if Packmol was useful:
L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez,
PACKMOL: A package for building initial configurations for
molecular dynamics simulations.
Journal of Computational Chemistry, 30:2157-2164,2009.
################################################################################
Solution written to file: system_init.pdb
--------------------------------------------------------------------------------
Running time: 0.223801002 seconds.
--------------------------------------------------------------------------------
-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
Working dir: /home/adit/MySoftware/CMMDE/examples/larutan/UreaAirAmonia/SistemLarutan
Command line:
gmx msd -f nptp.trr -s nptp.tpr -n SLV.ndx -o msd_SLV.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_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
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_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