Re: FEP on an amino acid ligand

From: Thomas Albers (
Date: Wed Jan 23 2013 - 07:36:36 CST


> 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.

I did build a second .psf to give results equivalent to the first one,
and that has atoms take off in strange directions, too. On my laptop
both systems behave as expected, on our cluster they do not, you see
atoms experience weird forces. This is a bug in NAMD.


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