Re: FEP on an amino acid ligand

From: JC Gumbart (
Date: Wed Jan 23 2013 - 08:24:25 CST

Explain in precise detail how you built the PSF. Likely you are missing some needed terms.

On Jan 23, 2013, at 8:36 AM, Thomas Albers wrote:

> Hello!
>> 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.
> Thomas

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