[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault

Steve Vivian svivian at uwo.ca
Wed Mar 9 04:13:06 CET 2011

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.

Steve Vivian.
svivian at uwo.ca

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