Re: FEP on an amino acid ligand

From: Thomas Albers (
Date: Tue Jan 22 2013 - 16:36:59 CST


>> 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.


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