[gmx-users] step 0Segmentation fault: 11

[Justin Lemkul]

On 11/26/13 6:31 PM, Valentina wrote:
> The problems I have eliminated:
>
> 1. Number of processors and threads - I am running on 1
> 2. Atomic overlap - none I have checked my bonded wells and my atomic
> distances are very similar. The  init was originally minimised with DFT.
> 3. LINCS - I get same error if I run with or without constraints
> 4. periodic_molecule - I should run with yes, but I tried to turn it off -
> no difference
> 5. Gromacs version - I tried on both 4.5.5 and 4.6.2
> 6. Machine specific - I have started on Mac, but now I am on Linux cluster.
>

The only possibility that remains is your tabulated potentials.

>
> Also my previous post shows the pressure 0. This is confusing! After energy
> minimisation my system's coordinates are 0 on z-axis. I changed that and now
> my md.log ends with a rather large pressure.
>

All of your quantities are completely unphysical, so picking out any one of them 
isn't necessarily indicative of anything.

-Justin

> Started mdrun on node 0 Tue Nov 26 23:23:27 2013
>
>             Step           Time         Lambda
>                0        0.00000        0.00000
>
> There were 58 inconsistent shifts. Check your topology
> Grid: 3 x 3 x 3 cells
>     Energies (kJ/mol)
>       Tab. Bonds    Tab. Angles        LJ (SR)   Coulomb (SR)      Potential
>      1.77548e+10    1.26662e+12    8.91352e+02   -1.08403e+05    1.28437e+12
>      Kinetic En.   Total Energy    Temperature Pressure (bar)
>      1.39515e+16    1.39528e+16    5.95027e+15    3.13627e+16
>
>
> I am lost with this error - help would be very appreciated.
> Thank you,
> V
>
>
> --
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>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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