From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Apr 06 2006 - 00:39:41 CDT
could you also please give us your pme and periodic cell parameters?
Also, I assume that you're seeing the simulation crash from these problems?
Chang, Christopher wrote:
> 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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