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
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