AMBER Archive (2005)

Subject: Re: AMBER: RE: gaff sugar residue instability

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 22 2005 - 13:40:18 CST

On Tue, Nov 22, 2005, hayden wrote:
>
> I have run dynamics on the molecule beginning at 0 K with high coupling to
> the heat bath (ntt=1) and gradually relaxed the restraints on the molecule
> over time. Once it was producing steady dynamics I removed the restraints
> and performed ordinary dynamics at 300K for 300 picoseconds. I then took
> this structure and minimized it to produce my final structure. However, the
> problem is that if I run dynamics on this minimized construct at higher
> temperatures (say 350 K) I get blow outs.

It would be helpful to know what you mean by the term "blow out". Look for
any hydrogens you have with zero van der Waals radii: these can be
troublesome, and usually require that SHAKE be turned on.

...good luck...dac
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