AMBER Archive (2003)

Subject: RE: non-periodic system

From: Yong Duan (yduan_at_udel.edu)
Date: Wed May 21 2003 - 22:24:01 CDT

Also,

The system, protein in a water ball, can mimic infinitely dilute
solution which is needed sometimes. Periodic boxes can not do that.

yong

> -----Original Message-----
> From: Michael Crowley [mailto:crowley_at_scripps.edu]
> Sent: Wednesday, May 21, 2003 7:27 PM
> To: Ioana Cozmuta
> Cc: amber_at_heimdal.compchem.ucsf.edu
> Subject: Re: non-periodic system
>
>
> Dear Ioana,
> I am curious to know what the meaning of pressure is
> in a non-periodic system. How does one model the "pressure"
> in a non-periodic system? Where is the external (constant)
> pressure coming from? What is the non-periodic NPT model in NAMD?
>
> THanks
> Mike
>
> -----------------------------------------------------------------
> Physical mail: Dr. Michael F. Crowley
> Department of Molecular Biology, TPC6
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, California 92037
>
> Electronic mail: crowley_at_scripps.edu
> Telephone: 858/784-9290
> Fax: 858/784-8688
> -----------------------------------------------------------------
>
>
>