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.
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 -- View this message in context: http://gromacs.5086.x6.nabble.com/step-0Segmentation-fault-11-tp5012832p5012834.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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