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,

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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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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