[gmx-users] Segmentation fault - Implicit solvent

[Steven Neumann]

On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

>
>
>  On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:
>
>>
>>
>>  On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul <jalemkul at vt.edu>wrote:
>>
>>>
>>>
>>> Steven Neumann wrote:
>>>
>>>> Dear Gmx Users,
>>>>  I am trying to run nvt simulation (equilibration) of the protein in
>>>> implicit solvent. My mdp:
>>>>
>>>> integrator = md ; leap-frog integrator
>>>>
>>>> nsteps = 1000000 ; 0.0005 * 1000000 = 0.5 ns
>>>>
>>>> dt = 0.0005 ; 0.5 fs
>>>>
>>>> ; Output control
>>>>
>>>> nstxout = 10000
>>>>
>>>> nstxtcout = 10000 ; xtc compressed trajectory output every 2 ps
>>>>
>>>> nstenergy = 10000 ; save energies every 2 ps
>>>>
>>>> nstlog = 10000 ; update log file every 2 ps
>>>>
>>>> ; Bond parameters
>>>>
>>>> continuation = no
>>>>
>>>> constraints = none
>>>>
>>>> ; Neighborsearching
>>>>
>>>> ns_type = simple ; search neighboring grid cells
>>>>
>>>> nstlist = 0 ; 10 fs
>>>>
>>>> rlist = 0 ; short-range neighborlist cutoff (in nm)
>>>>
>>>> ; Infinite box with no cutoffs
>>>>
>>>> pbc = no
>>>>
>>>> rcoulomb = 0 ; short-range electrostatic cutoff (in nm)
>>>>
>>>> coulombtype = cut-off
>>>>
>>>> vdwtype = cut-off
>>>>
>>>> rvdw = 0 ; short-range van der Waals cutoff (in nm)
>>>>
>>>> epsilon_rf = 0
>>>>
>>>> comm_mode = angular ; remove angular and com motions
>>>>
>>>> ; implicit solvent
>>>>
>>>> implicit_solvent = GBSA
>>>>
>>>> gb_algorithm = OBC
>>>>
>>>> gb_epsilon_solvent = 80.0
>>>>
>>>> sa_surface_tension = 2.25936
>>>>
>>>> rgbradii = 0
>>>>
>>>> sa_algorithm = Ace-approximation
>>>>
>>>> nstgbradii = 1
>>>>
>>>> ; Temperature coupling is on
>>>>
>>>> Tcoupl = v-rescale
>>>>
>>>> tau_t = 0.1
>>>>
>>>> tc_grps = system
>>>>
>>>> ref_t = 298
>>>>
>>>> ; Velocity generation
>>>>
>>>> gen_vel = yes ; Velocity generation is on
>>>>
>>>> gen_temp = 298.0
>>>>
>>>> gen_seed = -1
>>>>
>>>> Then after grompp I am trying to run the simulation on the cluster:
>>>>
>>>> mdrun -pd -deffnm nvt500ps
>>>>
>>>> My log file:
>>>>
>>>> Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1#
>>>>
>>>> Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision)
>>>>
>>>> Starting 8 threads
>>>>
>>>> Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1#
>>>>
>>>> Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1#
>>>>
>>>> Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1#
>>>>
>>>> starting mdrun 'Protein'
>>>>
>>>> 1000000 steps, 500.0 ps.
>>>>
>>>> Segmentation fault
>>>>
>>>>
>>>> Do you have any clue what is happening?
>>>>
>>>>
>>> Try running in serial or with a maximum of 2 threads.  Your problem
>>> could be related to http://redmine.gromacs.org/**issues/777<http://redmine.gromacs.org/issues/777>.
>>>  You will need to upgrade to 4.5.5 (serial should work on 4.5.4).
>>>
>>> -Justin
>>>
>>>
>> Thank you. What do you mean by running in serial? Well... with 2 threads
>> it does not make sense to use implicit solvent. Will 4.5.5 resolve this
>> problem?
>>
>>
>
> Indeed, it works in serial. Will version 4.5.5 resolve it run it on e.g.
> 12 nodes?
>
>

Sorry, the same problem :


Initial temperature: 298.398 K

Started mdrun on node 0 Thu Mar 1 15:56:04 2012

Step Time Lambda

0 0.00000 0.00000

Energies (kJ/mol)

Bond U-B Proper Dih. Improper Dih. CMAP Dih.

2.27391e+02 4.27461e+02 1.27733e+03 2.73432e+01 -6.95645e+02

GB Polarization Nonpolar Sol. LJ-14 Coulomb-14 LJ (SR)

inf 3.59121e+02 6.85627e+02 3.68572e+04 -7.57140e+02

Coulomb (SR) Potential Kinetic En. Total Energy Conserved En.

-3.30643e+04 inf nan nan nan

Temperature Pressure (bar)

nan 0.00000e+00

>
> -
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120301/a7aec092/attachment.html>