Small molecule simulation error NAMD

From: Chathuranga Siriwardhana (
Date: Mon Feb 22 2021 - 17:28:35 CST

Hi NAMD users,
I'm trying to see the interaction of a small molecule with a protein in
NAMD. As the simulation starts the following error appears;

ERROR: Margin is too small for 1 atoms during timestep 1004.
ERROR: Incorrect nonbonded forces and energies may be calculated!
ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000, atom
310 of 311 on patch 0 pe 1)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on
patch 0 pe 1).
FATAL ERROR: Exiting prematurely; see error messages above.

Atom 37 is a lone pair on Chlorine in the small molecule. Any help is
really appreciated.


*Chathuranga Siriwardhana*
Justin Legleiter Laboratory
West Virginia University
Department of chemistry
Clark Hall, Room 561
Morgantown, WV 26505

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