I usually equilibrate by doing initial heating with NVT, then bring the
system up to pressure with NPT. If I go straight to NPT my systems typically
explode. I too have explicit waters and PME. I think maybe things just may
be a bit more touchy if you go straight to NPT. I only usually run 10 ps of
initial NVT, anyway.
David
On 11/29/05, Vlad Cojocaru <Vlad.Cojocaru.eml-r.villa-bosch.de> wrote:
>
> Dear ambers,
>
> I have had many times a question in my mind when doing equilibrations
> on periodic systems with explicit waters (PME). In the amber manual it
> is recommended to do the heating step (first step of equilibration) at
> constant volume rather than constant pressure....However, I have used
> both ways and the systems that I worked on equilibrated properly in both
> cases.
> So, I was wondering about the background of this recommendation in
> the amber manual (page 98 under NTB). Could somebody explain in few
> words why it is recommended to do the heating step at constant volume?
>
> Best wishes
> vlad
> --
>
>
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Villa Bosch
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
> Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru.eml-r.villa-bosch.de
> <mailto:Vlad.Cojocaru.eml-r.villa-bosch.de>
> Additional info: my home page
> <http://projects.villa-bosch.de/mcm/people/cojocaru/>
>
>
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Received on Tue Nov 29 2005 - 19:53:01 PST
