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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/UreaAir/slurm-2613.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)
cp: cannot stat 'urea.mol2': No such file or directory
Cannot open file (urea_mod.mol2) with mode (r).
No such file or directory
-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: ./water_mod.mol2
Reading MOLECULE named SLV
Loading parameters: ./water.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: water_gaff.pdb
Quit
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
-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: ../water/water.lib
Loading parameters: ../water/water.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)
total atoms in file: 404
SLV SYSTEM URA gaff
Checking Unit.
/home/adit/miniconda3/bin/teLeap: Warning!
The unperturbed charge of the unit (-0.013100) is not integral.
/home/adit/miniconda3/bin/teLeap: Warning!
The unperturbed charge of the unit (-0.013100) 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 39 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 100
URA 13
)
(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 404 atoms
No velocities found
system size : 1.629 1.633 1.639 (nm)
diameter : 2.578 (nm)
center : -0.034 -0.002 -0.022 (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 : 0.845 0.813 0.834 (nm)
new center : 0.811 0.811 0.811 (nm)
new box vectors : 1.623 1.623 1.623 (nm)
new box angles : 90.00 90.00 90.00 (degrees)
new box volume : 4.27 (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 1209.00
There were 2 notes
Setting the LD random seed to 2143280071
Generated 21 of the 21 non-bonded parameter combinations
Generated 21 of the 21 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'system'
Analysing residue names:
There are: 113 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 0.116 0.116 0.116
Estimate for the relative computational load of the PME mesh part: 0.35
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 1395 steps
Potential Energy = -6.4208286e+03
Maximum force = 9.5925690e+01 on atom 381
Norm of force = 2.2167133e+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 1395.000 Last frame 0 time 1395.000
Analyzed 1 frames, last time 1395.000
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 1204]:
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 1204]:
For energy conservation with LINCS, lincs_iter should be 2 or larger.
Number of degrees of freedom in T-Coupling group rest is 957.00
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 -5902363
Generated 21 of the 21 non-bonded parameter combinations
Generated 21 of the 21 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'system'
turning H bonds into constraints...
Analysing residue names:
There are: 113 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 12x12x12, spacing 0.135 0.135 0.135
Estimate for the relative computational load of the PME mesh part: 0.32
This run will generate roughly 9 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'
100000 steps, 100.0 ps.
step 0 step 100, remaining wall clock time: 24 s step 200, remaining wall clock time: 24 s step 300, remaining wall clock time: 23 s step 400, remaining wall clock time: 23 s step 500, remaining wall clock time: 23 s step 600, remaining wall clock time: 23 s step 700, remaining wall clock time: 23 s step 800, remaining wall clock time: 23 s step 900, remaining wall clock time: 23 s step 1000, remaining wall clock time: 23 s step 1100, remaining wall clock time: 23 s step 1200, remaining wall clock time: 23 s step 1300, remaining wall clock time: 23 s step 1400, remaining wall clock time: 23 s step 1500, remaining wall clock time: 23 s step 1600, remaining wall clock time: 23 s step 1700, remaining wall clock time: 23 s step 1800, remaining wall clock time: 23 s step 1900, remaining wall clock time: 23 s step 2000, remaining wall clock time: 23 s step 2100, remaining wall clock time: 23 s step 2200, remaining wall clock time: 23 s step 2300, remaining wall clock time: 23 s step 2400, remaining wall clock time: 23 s step 2500, remaining wall clock time: 23 s step 2600, remaining wall clock time: 22 s step 2700, remaining wall clock time: 22 s step 2800, remaining wall clock time: 22 s step 2900, remaining wall clock time: 22 s step 3000, remaining wall clock time: 22 s step 3100, remaining wall clock time: 22 s step 3200, remaining wall clock time: 22 s step 3300, remaining wall clock time: 22 s step 3400, remaining wall clock time: 22 s step 3500, remaining wall clock time: 22 s step 3600, remaining wall clock time: 22 s step 3700, remaining wall clock time: 22 s step 3800, remaining wall clock time: 22 s step 3900, remaining wall clock time: 22 s step 4000, remaining wall clock time: 22 s step 4100, remaining wall clock time: 22 s step 4200, remaining wall clock time: 22 s step 4300, remaining wall clock time: 22 s step 4400, remaining wall clock time: 22 s step 4500, remaining wall clock time: 22 s step 4600, remaining wall clock time: 22 s step 4700, remaining wall clock time: 22 s step 4800, remaining wall clock time: 22 s step 4900, remaining wall clock time: 22 s step 5000, remaining wall clock time: 22 s step 5100, remaining wall clock time: 22 s step 5200, remaining wall clock time: 22 s step 5300, remaining wall clock time: 22 s step 5400, remaining wall clock time: 22 s step 5500, remaining wall clock time: 22 s step 5600, remaining wall clock time: 22 s step 5700, remaining wall clock time: 22 s step 5800, remaining wall clock time: 22 s step 5900, remaining wall clock time: 22 s step 6000, remaining wall clock time: 22 s step 6100, remaining wall clock time: 22 s step 6200, remaining wall clock time: 22 s step 6300, remaining wall clock time: 22 s step 6400, remaining wall clock time: 22 s step 6500, remaining wall clock time: 21 s step 6600, remaining wall clock time: 21 s step 6700, remaining wall clock time: 21 s step 6800, remaining wall clock time: 21 s step 6900, remaining wall clock time: 21 s step 7000, remaining wall clock time: 21 s step 7100, remaining wall clock time: 21 s step 7200, remaining wall clock time: 21 s step 7300, remaining wall clock time: 21 s step 740
Writing final coordinates.
step 100000, 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: 24.695 24.695 100.0
(ns/day) (hour/ns)
Performance: 349.871 0.069
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 1204]:
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 957.00
There was 1 note
There was 1 warning
Setting the LD random seed to -353377329
Generated 21 of the 21 non-bonded parameter combinations
Generated 21 of the 21 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'system'
turning H bonds into constraints...
Setting gen_seed to -17893746
Velocities were taken from a Maxwell distribution at 298.15 K
Analysing residue names:
There are: 113 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 0.719 nm, buffer size 0.008 nm
Set rlist, assuming 4x4 atom pair-list, to 0.711 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 0.135 0.135 0.135
Estimate for the relative computational load of the PME mesh part: 0.36
This run will generate roughly 5 Mb of data
Reading file nvt.tpr, VERSION 2021.3 (single precision)
Changing nstlist from 10 to 80, rlist from 0.711399 to 0.800399
Using 1 MPI thread
Using 1 OpenMP thread
NOTE: Thread affinity was not set.
starting mdrun 'system'
100000 steps, 100.0 ps.
step 0 step 100, remaining wall clock time: 18 s step 200, remaining wall clock time: 18 s step 300, remaining wall clock time: 18 s step 400, remaining wall clock time: 18 s step 500, remaining wall clock time: 17 s step 600, remaining wall clock time: 17 s step 700, remaining wall clock time: 17 s step 800, remaining wall clock time: 17 s step 900, remaining wall clock time: 17 s step 1000, remaining wall clock time: 17 s step 1100, remaining wall clock time: 17 s step 1200, remaining wall clock time: 17 s step 1300, remaining wall clock time: 17 s step 1400, remaining wall clock time: 17 s step 1500, remaining wall clock time: 17 s step 1600, remaining wall clock time: 17 s step 1700, remaining wall clock time: 17 s step 1800, remaining wall clock time: 17 s step 1900, remaining wall clock time: 17 s step 2000, remaining wall clock time: 17 s step 2100, remaining wall clock time: 17 s step 2200, remaining wall clock time: 17 s step 2300, remaining wall clock time: 17 s step 2400, remaining wall clock time: 17 s step 2500, remaining wall clock time: 17 s step 2600, remaining wall clock time: 17 s step 2700, remaining wall clock time: 17 s step 2800, remaining wall clock time: 17 s step 2900, remaining wall clock time: 17 s step 3000, remaining wall clock time: 17 s step 3100, remaining wall clock time: 17 s step 3200, remaining wall clock time: 17 s step 3300, remaining wall clock time: 17 s step 3400, remaining wall clock time: 17 s step 3500, remaining wall clock time: 17 s step 3600, remaining wall clock time: 17 s step 3700, remaining wall clock time: 17 s step 3800, remaining wall clock time: 17 s step 3900, remaining wall clock time: 17 s step 4000, remaining wall clock time: 17 s step 4100, remaining wall clock time: 17 s step 4200, remaining wall clock time: 17 s step 4300, remaining wall clock time: 16 s step 4400, remaining wall clock time: 16 s step 4500, remaining wall clock time: 16 s step 4600, remaining wall clock time: 16 s step 4700, remaining wall clock time: 16 s step 4800, remaining wall clock time: 16 s step 4900, remaining wall clock time: 16 s step 5000, remaining wall clock time: 16 s step 5100, remaining wall clock time: 16 s step 5200, remaining wall clock time: 16 s step 5300, remaining wall clock time: 16 s step 5400, remaining wall clock time: 16 s step 5500, remaining wall clock time: 16 s step 5600, remaining wall clock time: 16 s step 5700, remaining wall clock time: 16 s step 5800, remaining wall clock time: 16 s step 5900, remaining wall clock time: 16 s step 6000, remaining wall clock time: 16 s step 6100, remaining wall clock time: 16 s step 6200, remaining wall clock time: 16 s step 6300, remaining wall clock time: 16 s step 6400, remaining wall clock time: 16 s step 6500, remaining wall clock time: 16 s step 6600, remaining wall clock time: 16 s step 6700, remaining wall clock time: 16 s step 6800, remaining wall clock time: 16 s step 6900, remaining wall clock time: 16 s step 7000, remaining wall clock time: 16 s step 7100, remaining wall clock time: 16 s step 7200, remaining wall clock time: 16 s step 7300, remaining wall clock time: 16 s step 740
Writing final coordinates.
step 100000, remaining wall clock time: 0 s
Core t (s) Wall t (s) (%)
Time: 19.142 19.142 100.0
(ns/day) (hour/ns)
Performance: 451.375 0.053
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 957.00
Last frame -1 time 100.000
There was 1 note
Setting the LD random seed to 2113600431
Generated 21 of the 21 non-bonded parameter combinations
Generated 21 of the 21 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'system'
turning H bonds into constraints...
Analysing residue names:
There are: 113 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 0.740 nm, buffer size 0.029 nm
Set rlist, assuming 4x4 atom pair-list, to 0.711 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 = 100 ps
Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 12x12x12, spacing 0.135 0.135 0.135
Estimate for the relative computational load of the PME mesh part: 0.36
This run will generate roughly 3 Mb of data
Reading file npt.tpr, VERSION 2021.3 (single precision)
Changing nstlist from 10 to 40, rlist from 0.711399 to 0.798399
Using 1 MPI thread
Using 1 OpenMP thread
NOTE: Thread affinity was not set.
starting mdrun 'system'
100000 steps, 200.0 ps.
step 0 step 100, remaining wall clock time: 19 s step 200, remaining wall clock time: 19 s step 300, remaining wall clock time: 19 s step 400, remaining wall clock time: 19 s step 500, remaining wall clock time: 18 s step 600, remaining wall clock time: 18 s step 700, remaining wall clock time: 18 s step 800, remaining wall clock time: 18 s step 900, remaining wall clock time: 18 s step 1000, remaining wall clock time: 18 s step 1100, remaining wall clock time: 18 s step 1200, remaining wall clock time: 18 s step 1300, remaining wall clock time: 18 s step 1400, remaining wall clock time: 18 s step 1500, remaining wall clock time: 18 s step 1600, remaining wall clock time: 18 s step 1700, remaining wall clock time: 18 s step 1800, remaining wall clock time: 18 s step 1900, remaining wall clock time: 18 s step 2000, remaining wall clock time: 18 s step 2100, remaining wall clock time: 18 s step 2200, remaining wall clock time: 18 s step 2300, remaining wall clock time: 18 s step 2400, remaining wall clock time: 18 s step 2500, remaining wall clock time: 18 s step 2600, remaining wall clock time: 18 s step 2700, remaining wall clock time: 18 s step 2800, remaining wall clock time: 18 s step 2900, remaining wall clock time: 18 s step 3000, remaining wall clock time: 18 s step 3100, remaining wall clock time: 18 s step 3200, remaining wall clock time: 18 s step 3300, remaining wall clock time: 18 s step 3400, remaining wall clock time: 18 s step 3500, remaining wall clock time: 18 s step 3600, remaining wall clock time: 18 s step 3700, remaining wall clock time: 18 s step 3800, remaining wall clock time: 18 s step 3900, remaining wall clock time: 18 s step 4000, remaining wall clock time: 18 s step 4100, remaining wall clock time: 18 s step 4200, remaining wall clock time: 18 s step 4300, remaining wall clock time: 18 s step 4400, remaining wall clock time: 18 s step 4500, remaining wall clock time: 18 s step 4600, remaining wall clock time: 18 s step 4700, remaining wall clock time: 18 s step 4800, remaining wall clock time: 18 s step 4900, remaining wall clock time: 18 s step 5000, remaining wall clock time: 18 s step 5100, remaining wall clock time: 18 s step 5200, remaining wall clock time: 18 s step 5300, remaining wall clock time: 18 s step 5400, remaining wall clock time: 18 s step 5500, remaining wall clock time: 18 s step 5600, remaining wall clock time: 18 s step 5700, remaining wall clock time: 18 s step 5800, remaining wall clock time: 18 s step 5900, remaining wall clock time: 17 s step 6000, remaining wall clock time: 17 s step 6100, remaining wall clock time: 17 s step 6200, remaining wall clock time: 17 s step 6300, remaining wall clock time: 17 s step 6400, remaining wall clock time: 17 s step 6500, remaining wall clock time: 17 s step 6600, remaining wall clock time: 17 s step 6700, remaining wall clock time: 17 s step 6800, remaining wall clock time: 17 s step 6900, remaining wall clock time: 17 s step 7000, remaining wall clock time: 17 s step 7100, remaining wall clock time: 17 s step 7200, remaining wall clock time: 17 s step 7300, remaining wall clock time: 17 s step 740
Writing final coordinates.
step 100000, remaining wall clock time: 0 s
Core t (s) Wall t (s) (%)
Time: 21.036 21.036 100.0
(ns/day) (hour/ns)
Performance: 821.460 0.029
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'ns_type'
NOTE 1 [file nvep.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 1209.00
NOTE 2 [file nvep.mdp]:
NVE simulation: will use the initial temperature of 224.048 K for
determining the Verlet buffer size
There were 2 notes
Setting the LD random seed to -1646010373
Generated 21 of the 21 non-bonded parameter combinations
Generated 21 of the 21 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'system'
Analysing residue names:
There are: 113 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 224.048 K
Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.002 nm
Set rlist, assuming 4x4 atom pair-list, to 0.711 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: 0.34
This run will generate roughly 0 Mb of data
Reading file nvep.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'
10000 steps, 5.0 ps.
step 0 step 100, remaining wall clock time: 2 s step 200, remaining wall clock time: 2 s step 300, remaining wall clock time: 2 s step 400, remaining wall clock time: 1 s step 500, remaining wall clock time: 1 s step 600, remaining wall clock time: 1 s step 700, remaining wall clock time: 1 s step 800, remaining wall clock time: 1 s step 900, remaining wall clock time: 1 s step 1000, remaining wall clock time: 1 s step 1100, remaining wall clock time: 1 s step 1200, remaining wall clock time: 1 s step 1300, remaining wall clock time: 1 s step 1400, remaining wall clock time: 1 s step 1500, remaining wall clock time: 1 s step 1600, remaining wall clock time: 1 s step 1700, remaining wall clock time: 1 s step 1800, remaining wall clock time: 1 s step 1900, remaining wall clock time: 1 s step 2000, remaining wall clock time: 1 s step 2100, remaining wall clock time: 1 s step 2200, remaining wall clock time: 1 s step 2300, remaining wall clock time: 1 s step 2400, remaining wall clock time: 1 s step 2500, remaining wall clock time: 1 s step 2600, remaining wall clock time: 1 s step 2700, remaining wall clock time: 1 s step 2800, remaining wall clock time: 1 s step 2900, remaining wall clock time: 1 s step 3000, remaining wall clock time: 1 s step 3100, remaining wall clock time: 1 s step 3200, remaining wall clock time: 1 s step 3300, remaining wall clock time: 1 s step 3400, remaining wall clock time: 1 s step 3500, remaining wall clock time: 1 s step 3600, remaining wall clock time: 1 s step 3700, remaining wall clock time: 1 s step 3800, remaining wall clock time: 1 s step 3900, remaining wall clock time: 1 s step 4000, remaining wall clock time: 1 s step 4100, remaining wall clock time: 1 s step 4200, remaining wall clock time: 1 s step 4300, remaining wall clock time: 1 s step 4400, remaining wall clock time: 1 s step 4500, remaining wall clock time: 1 s step 4600, remaining wall clock time: 1 s step 4700, remaining wall clock time: 1 s step 4800, remaining wall clock time: 1 s step 4900, remaining wall clock time: 1 s step 5000, remaining wall clock time: 1 s step 5100, remaining wall clock time: 0 s step 5200, remaining wall clock time: 0 s step 5300, remaining wall clock time: 0 s step 5400, remaining wall clock time: 0 s step 5500, remaining wall clock time: 0 s step 5600, remaining wall clock time: 0 s step 5700, remaining wall clock time: 0 s step 5800, remaining wall clock time: 0 s step 5900, remaining wall clock time: 0 s step 6000, remaining wall clock time: 0 s step 6100, remaining wall clock time: 0 s step 6200, remaining wall clock time: 0 s step 6300, remaining wall clock time: 0 s step 6400, remaining wall clock time: 0 s step 6500, remaining wall clock time: 0 s step 6600, remaining wall clock time: 0 s step 6700, remaining wall clock time: 0 s step 6800, remaining wall clock time: 0 s step 6900, remaining wall clock time: 0 s step 7000, remaining wall clock time: 0 s step 7100, remaining wall clock time: 0 s step 7200, remaining wall clock time: 0 s step 7300, remaining wall clock time: 0 s step 740
Writing final coordinates.
step 10000, remaining wall clock time: 0 s
NOTE: 17 % 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: 2.045 2.045 100.0
(ns/day) (hour/ns)
Performance: 211.244 0.114
Will write pdb: Protein data bank file
Reading file nvep.tpr, VERSION 2021.3 (single precision)
Reading file nvep.tpr, VERSION 2021.3 (single precision)
Group 0 ( System) has 404 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 Reading frame 3 time 0.750 -> frame 3 time 0.750 Reading frame 4 time 1.000 -> frame 4 time 1.000 Reading frame 5 time 1.250 -> frame 5 time 1.250 Reading frame 6 time 1.500 -> frame 6 time 1.500 Reading frame 7 time 1.750 -> frame 7 time 1.750 Reading frame 8 time 2.000 -> frame 8 time 2.000 Reading frame 9 time 2.250 -> frame 9 time 2.250 Reading frame 10 time 2.500 -> frame 10 time 2.500 Reading frame 11 time 2.750 Reading frame 12 time 3.000 Reading frame 13 time 3.250 Reading frame 14 time 3.500 Reading frame 15 time 3.750 Reading frame 16 time 4.000 Reading frame 17 time 4.250 Reading frame 18 time 4.500 Reading frame 19 time 4.750 Reading frame 20 time 5.000 -> frame 20 time 5.000 Last frame 20 time 5.000
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: /home/adit/opt/gromacs-2021.3/build/bin/gmx
Data prefix: /home/adit/opt/gromacs-2021.3 (source tree)
Working dir: /home/adit/MySoftware/CMMDE/test/larutan/SistemLarutan
Command line:
gmx select -f nvep.gro -s nvep.tpr -on SLV.ndx -select '(resname SLV)'
Reading file nvep.tpr, VERSION 2021.3 (single precision)
Reading file nvep.tpr, VERSION 2021.3 (single precision)
Reading frames from gro file 'system', 404 atoms.
Reading frame 0 time 0.000 Last frame 0 time 0.000
Analyzed 1 frames, last time 0.000
GROMACS reminds you: "I'd Be Water If I Could" (Red Hot Chili Peppers)
:-) 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: /home/adit/opt/gromacs-2021.3/build/bin/gmx
Data prefix: /home/adit/opt/gromacs-2021.3 (source tree)
Working dir: /home/adit/MySoftware/CMMDE/test/larutan/SistemLarutan
Command line:
gmx msd -f nvep.trr -s nvep.tpr -n SLV.ndx -o msd_SLV.xvg
Reading file nvep.tpr, VERSION 2021.3 (single precision)
Reading file nvep.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 Reading frame 3 time 0.750 Reading frame 4 time 1.000 Reading frame 5 time 1.250 Reading frame 6 time 1.500 Reading frame 7 time 1.750 Reading frame 8 time 2.000 Reading frame 9 time 2.250 Reading frame 10 time 2.500 Reading frame 11 time 2.750 Reading frame 12 time 3.000 Reading frame 13 time 3.250 Reading frame 14 time 3.500 Reading frame 15 time 3.750 Reading frame 16 time 4.000 Reading frame 17 time 4.250 Reading frame 18 time 4.500 Reading frame 19 time 4.750 Reading frame 20 time 5.000 Last frame 20 time 5.000
Used 1 restart points spaced 10 ps over 5 ps
GROMACS reminds you: "I'd Be Water If I Could" (Red Hot Chili Peppers)
Fitting from 0.5 to 4.5 ps
D[(resname_SLV)] 6.4232 (+/- 1.9949) 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: /home/adit/opt/gromacs-2021.3/build/bin/gmx
Data prefix: /home/adit/opt/gromacs-2021.3 (source tree)
Working dir: /home/adit/MySoftware/CMMDE/test/larutan/SistemLarutan
Command line:
gmx select -f nvep.gro -s nvep.tpr -on URA.ndx -select '(resname URA)'
Reading file nvep.tpr, VERSION 2021.3 (single precision)
Reading file nvep.tpr, VERSION 2021.3 (single precision)
Reading frames from gro file 'system', 404 atoms.
Reading frame 0 time 0.000 Last frame 0 time 0.000
Analyzed 1 frames, last time 0.000
GROMACS reminds you: "I'd Be Water If I Could" (Red Hot Chili Peppers)
:-) 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: /home/adit/opt/gromacs-2021.3/build/bin/gmx
Data prefix: /home/adit/opt/gromacs-2021.3 (source tree)
Working dir: /home/adit/MySoftware/CMMDE/test/larutan/SistemLarutan
Command line:
gmx msd -f nvep.trr -s nvep.tpr -n URA.ndx -o msd_URA.xvg
Reading file nvep.tpr, VERSION 2021.3 (single precision)
Reading file nvep.tpr, VERSION 2021.3 (single precision)
Select a group to calculate mean squared displacement for:
Group 0 ( (resname_URA)) has 104 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 Reading frame 3 time 0.750 Reading frame 4 time 1.000 Reading frame 5 time 1.250 Reading frame 6 time 1.500 Reading frame 7 time 1.750 Reading frame 8 time 2.000 Reading frame 9 time 2.250 Reading frame 10 time 2.500 Reading frame 11 time 2.750 Reading frame 12 time 3.000 Reading frame 13 time 3.250 Reading frame 14 time 3.500 Reading frame 15 time 3.750 Reading frame 16 time 4.000 Reading frame 17 time 4.250 Reading frame 18 time 4.500 Reading frame 19 time 4.750 Reading frame 20 time 5.000 Last frame 20 time 5.000
Used 1 restart points spaced 10 ps over 5 ps
GROMACS reminds you: "I'd Be Water If I Could" (Red Hot Chili Peppers)
Fitting from 0.5 to 4.5 ps
D[(resname_URA)] 3.9640 (+/- 3.7993) 1e-5 cm^2/s
Suhu: 298.1500 K
0.7113990804113833
Membuat sistem larutan menggunakan PACKMOL
================================================================================
tolerance 2.5
filetype pdb
output system_init.pdb
structure ../water/water_gaff.pdb
number 100
inside cube -8.113990804113833 -8.113990804113833 -8.113990804113833 16.227981608227665
resnumbers 3
end structure
structure ../urea/URA_gaff.pdb
number 13
inside cube -8.113990804113833 -8.113990804113833 -8.113990804113833 16.227981608227665
resnumbers 3
end structure
================================================================================
Melakukan perhitungan MSD untuk pelarut
Melakukan perhitungan MSD untuk terlarut, masukkan masing-masing terlarut