On 6/27/13 3:16 PM, Sapna Sarupria wrote:
Thanks Justin for the response. I thought of that too but was not sure if
that could alone be attributed to the crash. There is no obvious reason why
it should happen given Gromacs has typically been quite stable. This is
quite a straightforward system...but perhaps it is the version. I am able
to run other simulations in this version with similar set up and therefore,
I wonder what is going wrong.
Without an actual backtrace from gdb, there's not much to go on, but then too,
the development team isn't going to try to fix anything about 4.5.4 that
presumably has already been fixed. The most obvious culprit in the .mdp file
below is the combination of velocity generation and Nose-Hoover; it's not a very
stable combination.
-Justin
On Thu, Jun 27, 2013 at 3:05 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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<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use an outdated version (4.5.4) when a slightly less outdated version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<http://www.gromacs.org/Documentation/Errors>
------------------------------**-------------------------
*********** End Error Message *************
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==============================**==========
Justin A. Lemkul, Ph.D.
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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