[gmx-users] Gromacs 4.5.4 and Gromacs 4.5.5 give different results
Justin Lemkul
jalemkul at vt.edu
Thu Jun 27 21:21:50 CEST 2013
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 <jalemkul at 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 use an outdated version (4.5.4) when a slightly less outdated version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 *************
>>>
>>>
>>>
>>> --
>>> View this message in context: http://gromacs.5086.x6.nabble.**
>>> com/Gromacs-4-5-4-and-Gromacs-**4-5-5-give-different-results-**
>>> tp5009424.html<http://gromacs.5086.x6.nabble.com/Gromacs-4-5-4-and-Gromacs-4-5-5-give-different-results-tp5009424.html>
>>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>>>
>>>
>> --
>> ==============================**==========
>>
>> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>>
>> --
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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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