AMBER Archive (2002)

Subject: Re: Constant pressure equilibration in a system with a solvent cap

From: David Smith (David.Smith_at_cup.uni-muenchen.de)
Date: Fri Sep 27 2002 - 11:11:19 CDT

dianah_at_unm.edu wrote:
>
> Hi,
>
> we used the solvate cap command to solvate a sphere of 30 Angstroms of
> water around the region of interest of our large DNA-protein system. Is
> it possible to run a constant pressure equilibration run with a
> solvated cap? That is, will the radius(volume) of the solvated cap
> adjust to achieve a constant pressure, or is the radius of the solvated
> cap fixed?

I don't know if this will be of any use but my way around this was as
follows:

I ran a constant pressure equilibration of my system in a periodic box
of water until I got a good density.
I then cut out a sphere of the radius I wanted and used it in my
non-periodic (droplet) calculations.

If you are interested and need any help with this procedure, please feel
free to ask.

Good luck.

 
---------------------------------------
Dr. David Smith
Department of Chemistry
Ludwig Maximilians University
Butenandt-Str. 5-13, D-81377 Munich
Germany
Tel.: +49 (0)89 2180 7740
Fax.: +49 (0)89 2180 7738
e-mail: David.Smith_at_cup.uni-muenchen.de
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