Bizarre atom behavior

From: Chang, Christopher (
Date: Wed Apr 05 2006 - 11:35:54 CDT


   We are trying to develop parameters for some metallocluster residues,
and are testing them with NAMD v2.6b1. At one point during the
simulation, one atom (a cyanide carbon attached to Fe and N) appears to
rocket off for no apparent reason! Three consecutive snapshots 1 fs
apart show the Fe-C-N angle to change from 180 to 61.7 to 35.9 degrees,
and the C-N bond length from 1.2 to 3.2 to 5.5 Angstroms. The triple
bond to the nitrogen atom has a force constant of ~ 2300 kcal/mol/A2,
yet this atom doesn't move appreciably. The dynamics behavior seems OK
right until this moment.

T=303 K
1 fs timestep
1-4 scaling=1.0
10/12/14 switchdist/cutoff/pairlistdist (switching on)
water rigid (Settle)
PME electrostatics

I have tried Langevin dynamics with 20 ps-1 and 5 s-1 damping constants,
Temperature Coupling, and velocity rescaling, with and without pressure
control by either Nose-Hoover or Berendsen (no flexible cell). I
consistently see atoms exceeding allowed velocity maxima--these 3
snapshots are an example.

Question: Has anyone else seen this type of behavior before? If so, what
are the possible (or better yet, likely) causes? Although my first
thought is lousy parameters, I wouldn't expect so abrupt a change;
furthermore, minimization proceeds without incident, and the affected
atoms vary from run to run.

Thanks in advance,


Christopher H. Chang, Ph.D.
Research Associate
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007

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