On 6/27/13 2:30 PM, sarupria wrote:
Hello all,
I have a naphthalene + water system which I want to run a NPT simulation of.
The system has been energy mininimized. When I run the NPT simulation using
gromacs 4.5.5 the simulation runs fine, but when I attempt to run the same
simulation using 4.5.4 it crashes with lincs error. We have tried various
things like energy minimizing multiple times using 4.5.4 but it still
crashes. I have also changed the thermostat and barostat to Berendsen, the
problem persists.
Has anything changed between the two versions that could lead to this
trouble? I am pasted the mdp file below and also the last few lines of the
error message I get from Gromacs 4.5.4.
Well, according to the release notes
(http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x), in version
4.5.5:
"Many small fixes which avoid termination with fatal errors or crashes in mdrun
and tools."
Small bugs are constantly getting fixed. I see no compelling reason to use an
outdated version (4.5.4) when a slightly less outdated version (4.5.5) works
correctly.
-Justin
Thanks for your help.
Sapna
************ MDP FILE *********
title = NPH + water ; a string
dt = 0.002 ; time step
nsteps = 12500000 ; number of steps
comm-grps = system
comm-mode = Linear
nstcomm = 10 ; reset c.o.m. motion
nstxout = 000 ; write coords
nstvout = 000 ; write velocities
nstlog = 2500 ; print to logfile
nstenergy = 500 ; print energies
xtc_grps = System
nstxtcout = 1000
nstlist = 10 ; update pairlist
ns_type = grid ; pairlist method
coulombtype = PME
rvdw = 1.00 ; cut-off for vdw
rcoulomb = 1.00 ; cut-off for coulomb
rlist = 1.00 ; cut-off for coulomb
Tcoupl = Nose-Hoover
ref_t = 280.0
tc-grps = System
tau_t = 0.5
DispCorr = EnerPres ; long range correction
gen_vel = yes ; generate init. vel
gen_temp = 280 ; init. temp.
gen_seed = 372340 ; random seed
constraints = h-bonds ; constraining bonds with H
constraint_algorithm = lincs
refcoord-scaling = no
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic ; pressure geometry
tau_p = 1.0 ; p-coupoling time
compressibility = 4.5e-5 ; compressibility
ref_p = 1.0 ; ref pressure
nsttcouple = 1
nstpcouple = 1
***************** END MDP File ***************
*********** Error Message *************
Program mdrun_sp, VERSION 4.5.4
Source code file: constr.c, line: 176
Fatal error:
Too many LINCS warnings (4811)
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
*********** End Error Message *************
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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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