[gmx-users] warnings in energy minimization

James Lord jjamesgreen110 at gmail.com
Sat May 16 06:14:37 CEST 2015

Hi all,
I am using Justin's minim.mdp to energy minimize my system and I am getting
these warnings,Should I care about them? It is saying that my simulation
may not be stable?

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000

WARNING: Listed nonbonded interaction between particles 5312 and 5315
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.

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