[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    
> 2.71260e+03
>         LJ (SR)              Disper. corr.           Coulomb (SR)   
> Coul. recip.             Position Rest.
>     1.49883e+04   -1.42684e+03       -2.78329e+05       -1.58540e+05   
>      2.57100e+00
>       Potential            Kinetic En.               Total Energy      
>             Conserved En.               Temperature
>    -4.20446e+05    *1.41436e+14        1.41436e+14        1.41436e+14    
>         1.23343e+12*
>  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.


> Regards,
> Steve Vivian.
> svivian at uwo.ca


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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