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
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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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Received on Wed Nov 12 2003 - 01:53:01 PST
