RE: Minimization/Equilibrium problem, atoms moving too fast

From: adrian palacios (
Date: Thu Jul 18 2013 - 19:58:47 CDT

Well, my procedure to define the cell dimensions is running the "measure minmax $sel" where sel is the selection of the water box and using the diference between those vectors as each of the cell dimensions, for example, if it gives me {-80.5 . .} and {80.4 . .} I give a cell vector {161 0 0} as I did in my configuration file, trying to give numbers rounded to the greater integer. And sorry for my incorrect expression, I was thinking of the absolute value of energy, but you are correct in that point.

Before you answered I looked for the vdw "NAMD Plot" from the minimization log file and it does represent the greater contribution to this unstability, but how could I fix this? I tried running a similar system in a smaller box and it worked, but still is the second time I have this problem related to CaCl Ionization neutralizing the system.

Thanks for your reply, it was very accurate.

Adrian Palacios

Date: Thu, 18 Jul 2013 17:12:32 -0400
Subject: Re: namd-l: Minimization/Equilibrium problem, atoms moving too fast

>From the log, your energies actually go crazy low after minimization, not crazy high. And this seems to result from the ' VDW BOUNDARY' term. I'm not sure what this term applies to, but how confident are you in the cell dimensions you gave the system?

On Thu, Jul 18, 2013 at 4:28 PM, Adrian <> wrote:

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:30 CST