[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault
Justin A. Lemkul
jalemkul at vt.edu
Wed Mar 9 04:23:53 CET 2011
Steve Vivian wrote:
> New to Gromacs.
> Worked my way through the tutorial with relatively few issues until the
> Equilibration stage. My system blows up!!
> Returned to the Topology stage and rebuilt my system ensuring that I
> followed the procedure correctly for the InflateGro process. It appears
> to be correct, reasonable lipid area, no water inside my bilayer, vmd
> shows a structure which appears normal (although I am new to this).
> There are voids between bilayer and water molecules, but this is to be
> expected, correct?
> Energy Minimization repeatedly produces results within the expected range.
> Again system blows up at equilibration, step 0 segmentation fault.
> Regardless of whether I attempt the NVT or Anneal_Npt process (using the
> provided mdp files, including the updates for restraints on the protein
> and the lipid molecules).
> I have attempted many variations of the nvt.mdp and anneal_npt.mdp files
> hoping to resolve my issue, but with no success. I will post the log
> information from the nvt.mdp file included in the tutorial.
> Started mdrun on node 0 Tue Mar 8 15:42:35 2011
> Step Time Lambda
> 0 0.00000 0.00000
> Grid: 9 x 9 x 9 cells
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih.
> LJ-14 Coulomb-14
> 8.52380e+01 6.88116e+01 2.23939e+01 -3.03546e+01
> LJ (SR) Disper. corr. Coulomb (SR)
> Coul. recip. Position Rest.
> 1.49883e+04 -1.42684e+03 -2.78329e+05 -1.58540e+05
> Potential Kinetic En. Total Energy
> Conserved En. Temperature
> -4.20446e+05 *1.41436e+14 1.41436e+14 1.41436e+14
> Pres. DC (bar) Pressure (bar) Constr. rmsd
> -1.56331e+02 5.05645e+12 1.18070e+01
> As you can see the Potential Energy is reasonable, but the Kinetic
> Energy and Temperature seem unrealistic.
> I am hoping that this is enough information for a more experienced
> Gromacs user to provide guidance.
> Note: that I have tried all of the suggestions that I read on the
> mailing list and in the "blowing up" section of the manual, specifically:
> -reduced time steps in Equilibration Stages
> -reduced Fmax during EM stage (down as low as 100kJ which did not help)
> -modified neighbours list parameters
> Any help is appreciated.
> I can attach and forward any further information as required, please let
> me know.
Which Gromacs version are you using? It looks like you're running in serial, is
that correct? Otherwise, please provide your mdrun command line. If you're
using version 4.5.3 in serial, I have identified a very problematic bug that
seems to affect a wide variety of systems that could be related:
I have seen even the most robust tutorial systems fail as well, as some new lab
members experienced the same problem. The workaround is to run in parallel.
> Steve Vivian.
> svivian at uwo.ca
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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