From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Thu Apr 06 2006 - 16:40:04 CDT
Yes, the sim crashes with a message about certain atom velocities
(the errant atom as well as whatever it crashes into, if it does so)
exceeding a cutoff. The PME cell is 90 X 80 X 81, the periodic cell is
86.5 X 78.6 X 80.7.
I suspect this may be happening due to the van der Waals radius vs.
the equilibrium bond length. If the former were too large vs. the
latter, a small drift in one timestep might bring it pretty high up the
6-12 potential wall...?
> -----Original Message-----
> From: Peter Freddolino [mailto:petefred_at_ks.uiuc.edu]
> Sent: Wednesday, April 05, 2006 11:40 PM
> To: Chang, Christopher
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: Bizarre atom behavior
> Hi Chris,
> 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:
> > Hi,
> > 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
> > 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)
> > nonbondFreq=1
> > fullElectFrequency=2
> > stepspercycle=10
> > 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,
> > Chris
> > 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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