[gmx-users] simulation broke at 4.0.5 version
Chih-Ying Lin
chihying2008 at gmail.com
Thu Jan 7 07:50:49 CET 2010
Hi
I am using Gromacs version 4.0.5.
I put one protein in a simulation box with water molecules and CL- only.
My simulation broke at the step, Relaxation of solvent and hydrogen atom
position.
Here are the .top file, command, output of the grommp, pr.mdp.
anything wrong here?
Thank you
Lin
*[6YZ.top]*
[ molecules ]
; Compound #mols
Protein_A 1
SOL 6504
CL- 8
*Relaxation of solvent and hydrogen atom positions: Position restrained MD*
*[command]*
grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr
mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR
*[output of the grompp comand]*
grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr
:-) G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
:-) VERSION 4.0.5 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp_mpi (-:
Option Filename Type Description
------------------------------------------------------------
-f pr.mdp Input, Opt! grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c 6LYZ-EM-solvated.gro Input Structure file: gro g96 pdb tpr tpb
tpa
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-n index.ndx Input, Opt. Index file
-p 6LYZ.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o 6LYZ-PR.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file: edr ene
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings during input
processing
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
NOTE 1 [file pr.mdp, line unknown]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
processing topology...
Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3.itp
Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3nb.itp
Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3bon.itp
Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp
Generated 141 of the 1176 non-bonded parameter combinations
Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL-'
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 200 K
Reading position restraint coords from 6LYZ-EM-solvated.gro
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/aminoacids.dat
There are: 6512 OTHER residues
There are: 129 PROTEIN residues
There are: 0 DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for Acceleration containing 20841 elements
Making dummy/rest group for Freeze containing 20841 elements
Making dummy/rest group for VCM containing 20841 elements
Number of degrees of freedom in T-Coupling group Protein is 2618.00
Number of degrees of freedom in T-Coupling group Non-Protein is 39048.00
Making dummy/rest group for User1 containing 20841 elements
Making dummy/rest group for User2 containing 20841 elements
Making dummy/rest group for Or. Res. Fit containing 20841 elements
Making dummy/rest group for QMMM containing 20841 elements
T-Coupling has 2 element(s): Protein Non-Protein
Energy Mon. has 2 element(s): Protein Non-Protein
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): System
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
This run will generate roughly 3 Mb of data
writing run input file...
There was 1 note
Back Off! I just backed up 6LYZ-PR.tpr to ./#6LYZ-PR.tpr.1#
gcq#264: "RTFM" (B. Hess)
*[pr.mdp]*
**
; VARIOUS PREPROCESSING OPTIONS
title =
cpp = /lib/cpp
include =
define = -DPOSRES
; RUN CONTROL PARAMETERS
integrator = md
tinit = 0
dt = 0.001
nsteps = 5000
nstcomm = 0
; OUTPUT CONTROL OPTIONS
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 10
nstenergy = 1
nstxtcout = 0
xtc_precision = 1000
xtc-grps = System
energygrps = Protein Non-Protein
; NEIGHBORSEARCHING PARAMETERS
nstlist = 5
ns-type = Grid
pbc = xyz
rlist = 0.9
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = Reaction-Field
rcoulomb = 1.4
epsilon_rf = 78
epsilon_r = 1
vdw-type = Cut-off
rvdw = 1.4
; Temperature coupling
Tcoupl = Berendsen
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 200 200
; Pressure coupling
Pcoupl = No
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 200.0
gen_seed = 1735
; OPTIONS FOR BONDS
constraints = all-bonds
constraint-algorithm = Lincs
unconstrained-start = no
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
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