AW: FEP on an amino acid ligand

From: Norman Geist (
Date: Wed Jan 23 2013 - 01:21:09 CST

Did you check if the minimization was long enough? Try the namd plot plugion
in vmd to plot the total energy and see if it was converged and watch the
outfile for some messages like "moving bad contacs downhill" or "giving up
on x bad cotacts" which would indicate a really bad initial structure.
Additionally, as we work with computers and they produce errors, try to
rebuild the psf. I'm using the amber ff and rarely some strange behavior is
observed in my simulations. Rebuilding the topology file fixes the problem

Good luck
Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: [] Im
> Auftrag von Thomas Albers
> Gesendet: Dienstag, 22. Januar 2013 23:37
> An: Norman Geist
> Cc: Namd Mailing List
> Betreff: Re: namd-l: FEP on an amino acid ligand
> Hello!
> >> the simulation blows up within a few hundred timesteps. At constant
> >> pressure, NAMD complains about the periodic cell having become to
> >> small, and at constant volume one sees atoms moving too fast.
> >
> > This usually indicates that the periodic box is to small from the
> start.
> > Check if you got some atoms out of bounds. Remember that if the box
> is set
> > to small and the simulation starts, the atoms will be treated as
> wrapped and
> > so maybe superimposed with other atoms, or too close. This would
> cause the
> > two situations you mentioned.
> When you look at the trajectory you see CB of alanine take move in one
> direction. This is odd, and I'm not sure if the problem is with the
> input files, or if it is a strange bug in NAMD.
> Thomas

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:20:52 CST