From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Mon Feb 22 2021 - 17:34:17 CST
What version of NAMD are you using? Versions earlier than NAMD 2.14 don’t
support halogen lonepairs.
On Mon, Feb 22, 2021 at 17:31 Chathuranga Siriwardhana <ccs0019_at_mix.wvu.edu>
> 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
-- –––––––––––––––––––––––––––––––––––——————— Jeffrey Comer, PhD Associate Professor Department of Anatomy and Physiology Kansas State University Office: P-213 Mosier Hall Phone: 785-532-6311 Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!rrDOk0DOYvWUezF6gBZcQhAchOUxh-pBWJ5CQg3l3Aa5zw6NmQexSwR8nuRumTCXvA$
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