[gmx-users] Cyclohexane simulation problem
mohsen shahlaei
mohsenshahlaei at yahoo.com
Sun May 31 12:04:04 CEST 2015
Thank you Justin for prompt reply.I have been used coulombtype = Cut-off in my mdp file for Cyclohexane energy minimization but the results sound odd.I used cyclohexane density (0.824 g/ml) for calculating number of CHX molecules in a 10 nm3 (about 56 molecules). Then I used following command to make a box.gmx insert-molecules -ci chx.gro -nmol 56 -box 2.154434 2.154434 2.154434 -o chx_box.grochx.gro and chx.itp that I used are:
=============chx.itp ==================;
;
; This file was generated by PRODRG version AA100323.0717
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
;
;
[ moleculetype ]
; Name nrexcl
chx 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH1 1 chx CAA 1 0.000 14.0270
2 CH1 1 chx CAB 1 0.000 14.0270
3 CH1 1 chx CAE 1 0.000 14.0270
4 CH1 1 chx CAF 1 0.000 14.0270
5 CH1 1 chx CAD 1 0.000 14.0270
6 CH1 1 chx CAC 1 0.000 14.0270
[ bonds ]
; ai aj fu c0, c1, ...
1 2 2 0.152 5430000.0 0.152 5430000.0 ; CAA CAB
1 6 2 0.152 5430000.0 0.152 5430000.0 ; CAA CAC
2 3 2 0.152 5430000.0 0.152 5430000.0 ; CAB CAE
3 4 2 0.152 5430000.0 0.152 5430000.0 ; CAE CAF
4 5 2 0.152 5430000.0 0.152 5430000.0 ; CAF CAD
5 6 2 0.152 5430000.0 0.152 5430000.0 ; CAD CAC
[ pairs ]
; ai aj fu c0, c1, ...
1 4 1 ; CAA CAF
2 5 1 ; CAB CAD
3 6 1 ; CAE CAC
[ angles ]
; ai aj ak fu c0, c1, ...
2 1 6 2 109.5 520.0 109.5 520.0 ; CAB CAA CAC
1 2 3 2 109.5 520.0 109.5 520.0 ; CAA CAB CAE
2 3 4 2 109.5 520.0 109.5 520.0 ; CAB CAE CAF
3 4 5 2 109.5 520.0 109.5 520.0 ; CAE CAF CAD
4 5 6 2 109.5 520.0 109.5 520.0 ; CAF CAD CAC
1 6 5 2 109.5 520.0 109.5 520.0 ; CAA CAC CAD
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
3 2 1 6 1 0.0 5.9 3 0.0 5.9 3 ; dih CAE CAB CAA CAC
5 6 1 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CAD CAC CAA CAB
4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih CAF CAE CAB CAA
5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CAD CAF CAE CAB
6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih CAC CAD CAF CAE
1 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih CAA CAC CAD CAF
=================================chx.gro==================== PRODRG COORDS
6
1chx C AA 1 0.155 0.105 0.177
1chx C AB 2 0.100 0.247 0.184
1chx C AE 3 0.182 0.344 0.100
1chx C AF 4 0.330 0.339 0.137
1chx C AD 5 0.385 0.196 0.130
1chx C AC 6 0.303 0.100 0.214
0.48500 0.44400 0.31400===========================================================
Then I minimized the energy of generated box as follows:gmx grompp -f minim.mdp -c chx_box.gro -p chx_box.top -o em.tpr -maxwarn 1gmx mdrun -deffnm em -v
The warning I got in grompp runing was
WARNING 1 [file chx_box.top, line 58]:
336 non-matching atom names
atom names from chx_box.top will be used
atom names from chx_box.gro will be ignored
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are: 56 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 1005.00
This run will generate roughly 2 Mb of data
There was 1 note
There was 1 warning
-------------------------------------------------------
Program gmx, VERSION 5.0.4
Source code file: /home/mohsen/Downloads/gromacs-5.0.4/src/gromacs/gmxpreprocess/grompp.c, line: 2087
Fatal error:
Too many warnings (1), gmx terminated.
So I used -maxwarn 1
The chx_box ITP is==========================chx_box.itp=====================;
; File 'topol.top' was generated
; By user: mohsen (1000)
; On host: mohsen-All-Series
; At date: Wed May 20 12:09:46 2015
;
; This is a standalone topology file
;
; Created by:
; GROMACS: gmx pdb2gmx, VERSION 5.0.4
; Executable: /usr/local/gromacs/bin/gmx
; Library dir: /usr/local/gromacs/share/gromacs/top
; Command line:
; gmx pdb2gmx -f pep.gro -o peptide.gro -water spce
; Force field was read from the standard Gromacs share directory.
;
nrexcl=3
; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; octanol position restraints
#ifdef POSRES_CHX
#include "system.itp"
#endif
; Include water topology
#include "gromos53a6.ff/spce.itp"
#include "chx.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "gromos53a6.ff/ions.itp"
[ system ]
; Name
Gromacs Runs On Most of All Computer Systems in
[ molecules ]
; Compound #mols
chx 56
and the minim.mdp is as follows:===============================minim.itp=======================; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 100.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 500000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = Cut-off ; Treatment of long range electrostatic interactions
rcoulomb = 1 ; Short-range electrostatic cut-off
rvdw = 1 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)===========================================================
the results of energy minimization is as follows:writing lowest energy coordinates.
Back Off! I just backed up em.gro to ./#em.gro.19#
Steepest Descents converged to Fmax < 100 in 1025 steps
Potential Energy = 1.9984604e+03
Maximum force = 9.3209557e+01 on atom 181
Norm of force = 2.5035557e+01
NOTE: 19 % of the run time was spent in pair search,
you might want to increase nstlist (this has no effect on accuracy)
As it can be seen the potential energy is positive. Please let me know why and solution please.
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