[gmx-users] Segmentation fault - Implicit solvent
Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 1 18:43:17 CET 2012
Steven Neumann wrote:
>
>
> On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann <s.neumann08 at gmail.com
> <mailto:s.neumann08 at gmail.com>> wrote:
>
>
>
> On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann
> <s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>> wrote:
>
>
>
> On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto: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 :
>
I think, as stated in the redmine issue cited before, the limit is 2
threads/processors.
-Justin
>
> 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 <http://vt.edu/> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> 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. 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
========================================
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