AMBER Archive (2003)

Subject: Re: AMBER: Separation of a Water molecules

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Nov 11 2003 - 20:15:53 CST

this seems strange. you didn't give a lot of information.
what is the pressure at the start? at the end? are
you sure it is NTP? some information from the input
and output would help.

----- Original Message -----
From: "nabe" <watanabe-katsuhiro_at_hitachi-ul.co.jp>
To: <amber_at_scripps.edu>
Sent: Tuesday, November 11, 2003 7:59 PM
Subject: AMBER: Separation of a Water molecules

> Dear AMBER users.
>
> We have encountered the very serious problem. It is
> that the water molecules in the middle of MD
> separates. The links and explanations of pictures
> wrote below.
>
> Is a countermeasure in this phenomenon?
>
> Thanks.
>
> K. Watanabe
>
> +++++++++++++++++++++++++++++++++++++++
> Please look at files as
> http://www004.upp.so-net.ne.jp/nabekatsu/MD0.jpg
> (156 Kbytes)
> and
> http://www004.upp.so-net.ne.jp/nabekatsu/MD1.jpg
> (148 Kbytes).
>
> *MD0.jpg is before MD execution (t=0ps),
> and MD1.jpg is after MD execution (t=20ps).
>
> The important conditions of MD are
> - cell size ~ 80x80x80A^3
> - using WATBOX216 for water molecules
> - algorithm PME and NTP
> - using sander of amber5.
> +++++++++++++++++++++++++++++++++++++++
>
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