margin errors

From: Stern, Julie (
Date: Fri Jun 18 2004 - 14:48:36 CDT

   I'm running namd and am getting the following errors as its
ERROR: 10 margin violations detected since previous energy output.
ERROR: Margin is too small for 1 atoms during timestep #.
ERROR: Incorrect nonbonded forces and energies may be caculated!

Then is repeats during the simulation varying the timestep # and the
# of margin violations.

I did run minimization prior to this run, so I thought minimization
would take care of any bad contacts. This is a run on the
minimized structure.

What does this mean, what margin, and how do I get rid of it?


Julie Stern

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:42 CST