[gmx-users] Gromacs simulation of two or more peptide chain

Vytautas Rakeviius vytautas1987 at yahoo.com
Thu Aug 31 13:18:32 CEST 2017

Generally that means you starting system is seriously wrong.
Investigate atom 218 and surrounding area. Another atom really close or sth like that.

On Thursday, August 24, 2017, 9:36:37 PM GMT+3, Kalyanashis Jana <kalyan.chem.in at gmail.com> wrote:

Dear all,
I would like to run an MD simulation for two or more peptide chain. I got
the following error in the steepest descent energy minimization step. Could
you please suggest me, how can I do the MD simulation?

Steepest Descents:
  Tolerance (Fmax)  =  1.00000e+02
  Number of steps    =      200000

WARNING: Listed nonbonded interaction between particles 215 and 219
at distance 3f which is larger than the table limit 3f nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

Segmentation fault (core dumped)ot=        -nan Fmax= 8.56592e+05, atom=

Thanks with regards
Kalyanashis Jana
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