[gmx-users] grommp_md error
Moeed
lecielll at googlemail.com
Tue Jul 13 05:08:18 CEST 2010
Hello,
Sorry I did not paste the error message part properly. Initially I am trying
to study PE in vacuum (current box size 30*30*30 nm) and then I will solvate
the PE with Hexane.
NOTE 1 [file md-July11-NPTcompression.mdp, line unknown]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Opening library file /chem_soft/gromacs/share/gromacs/top/spc.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'polymer'
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
Making dummy/rest group for Acceleration containing 2896 elements
Making dummy/rest group for Freeze containing 2896 elements
Making dummy/rest group for Energy Mon. containing 2896 elements
Making dummy/rest group for VCM containing 2896 elements
Number of degrees of freedom in T-Coupling group Eth is 5373.22
Number of degrees of freedom in T-Coupling group EthB is 211.89
Number of degrees of freedom in T-Coupling group EthE is 211.89
Making dummy/rest group for User1 containing 2896 elements
Making dummy/rest group for User2 containing 2896 elements
Making dummy/rest group for XTC containing 2896 elements
Making dummy/rest group for Or. Res. Fit containing 2896 elements
Making dummy/rest group for QMMM containing 2896 elements
T-Coupling has 3 element(s): Eth EthB EthE
Energy Mon. has 1 element(s): rest
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): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
writing run input file...
There was 1 note
There was 1 warning
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: gmx_fatal.c, line: 481
Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
-------------------------------------------------------
"My Heart is Just a Muscle In a Cavity" (F. Black)
:-) G R O M A C S (-:
Gromacs Runs One Microsecond At Cannonball Speeds
:-) VERSION 4.0.7 (-:
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 (double precision) (-:
processing topology...
turning all bonds into constraints...
Analysing residue names:
There are: 240 OTHER residues
There are: 0 PROTEIN residues
There are: 0 DNA residues
Analysing Other...
This run will generate roughly 14 Mb of data
*********************************************************************************************************
Then I altered the tc groups in mdp file to Polymer and use n option in
grompp.
grompp -f md-July11-NPTcompression.mdp -c PE60_b4pr -p PE60.top -o PE60_md
-n index.ndx >& output.grompp_md
(actually I wanted to what how tc group names are based on? I thought they
come from residue names, then I changed index file [all] name to [polymer]
index file:
[ special ]
1 3
[ Polymer ]
1 2 3 4
error:******************************************************************
WARNING 1 [file md-July11-NPTcompression.mdp, line unknown]:
Unknown or double left-hand 'rvw-switch' in parameter file
checking input for internal consistency...
NOTE 1 [file md-July11-NPTcompression.mdp, line unknown]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Opening library file /chem_soft/gromacs/share/gromacs/top/spc.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Polymer'
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: readir.c, line: 1069
Fatal error:
358 atoms are not part of any of the T-Coupling groups
-------------------------------------------------------
"Rat-tat-tat Ka boom boom" (The Smashing Pumpkins)
:-) G R O M A C S (-:
Glycine aRginine prOline Methionine Alanine Cystine Serine
:-) VERSION 4.0.7 (-:
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 (double precision) (-:
processing topology...
turning all bonds into constraints...
******************************************************************************************************************
.
2- I have a question about doing NPT for compressing the system. Can I also
do NVT for a short time and when the chain has a more realistic structure ,
take that structure and change the volume myself? I am just asking for the
sake of learning.. This doesnt mean I am not going to do follow your
advise..
3- Also If I want to find the pressure which gives the size I want, I need
to wait till the end of simulation to see the volume (eg with g_energy) and
repeat this to find the desired volume by try and error?
Thanks :)
mdp file:
title = PE-Hexane
;define = -DPOSRES ; tells gromacs to perform position
restrained dynamics/include posre.itp into topology used for position
restraint
pbc = xyz ; use priodic BCs in all directions
; Run control
integrator = md ; type of dynamics algorithm. Here md uses
a leap-frog algorithm for integrating Newtons's eq of motion
dt = 0.002 ; in ps !
nsteps = 5000 ; length of simulation=
nsteps*dt
nstcomm = 1 ; frequency for center of mass motion
removal
; Output control
nstenergy = 100 ; frequency to write energies to energy
file. i.e., energies and other statistical data are stored every 10 steps
nstxout = 100 ; frequency to write
coordinates/velocity/force to output trajectory file. how often snapshots
are collected= nstxout*dt
nstvout = 100
nstfout = 0
nstlog = 100 ; frequency to write energies to log file
nstxtcout = 10 ; frequency to write coordinates to xtc
trajectory
; Neighbor searching
nstlist = 10 ; frequency to update neighbor list.
Neighborlist will be updated at least every 10 steps. Manual p80
ns_type = grid ; make a grid in the box and only check
atoms in neighboring grid cells when constructing a new neighbor list every
nstlist steps
; Electrostatics/VdW
coulombtype = Shift ; tells gromacs how to model
electrostatics. Coulomb/LJ potential is decreased over the whole range and
forces decay smoothly to zero between
vdw-type = Shift ; rcoulomb-switch/rvw-switch &
rcoulomb/rvdw
rcoulomb-switch = 0 ; where to start switching the Coulomb
potential
rvw-switch = 0 ; where to start switching the LJ
potential
; Cut-offs
rlist = 1.1 ; in nm. Cut-off distance for short-range
neighbor list
rcoulomb = 1.0 ; distance for coulomb cut-off
rvdw = 1.0 ; distance for coulomb cut-off
; Temperature coupling
Tcoupl = berendsen
tc-grps = polymer ;HEX ; groups to couple to
thermostat; Berendsen temperature coupling is on in these groups
tau_t = 0.1 ;0.1 ; time constant for T
coupling
ref_t = 300 ;300 ; reference T for coupling.
When you alter the T, don't forget to change the gen_temp for velocity
generation
; Pressure coupling
Pcoupl = berendsen ; Pressure coupling is not on
Pcoupltype = isotropic ; means the box expands and contracts
in all directions (x,y,z) in order to maintain the proper pressure
tau_p = 0.5 ; time constant for coupling in ps
compressibility = 4.5e-5 ; compressibility of solvent used in
simulation in 1/bar
ref_p = 1.0 ; reference P for coupling in bar
; Velocity generation Generate velocites is on at 300 K. Manual
p155
gen_vel = yes ; generate velocites according to Maxwell
distribution at T: gen_temp with random gen seed gen_seed
gen_temp = 300.0 ; T for Maxwell distribution
gen_seed = 173529 ; used to initialize random generator
for random velocities
; Bonds
constraints = all-bonds ; sets the LINCS constraint for all
bonds
constraint-algorithm = lincs
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