AMBER Archive (2003)

Subject: AMBER: ndfmin in belly runs

From: John (john.dalmaris_at_imperial.ac.uk)
Date: Thu Nov 13 2003 - 04:50:52 CST

Hello,

Following on from Rhonda's e-mail I would appreciate it if you could provide
me with some more information on the ndfmin when undertaking belly runs. I
have not encounter this in any belly run so I assume that sander set this to
0. Do we have to subtract the degrees of freedom lost due to belly from the
whole system? How does this change the ndfmin?

Many thanks for your feedback.

Cheers,

John

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Rhonda Torres
Sent: 12 November 2003 20:36
To: amber_at_scripps.edu
Cc: px208_at_nyu.edu
Subject: Re: AMBER: about some of the cards in Sander 7

Hi Pingna,

ntx=7 is O.K. for an MD restart.

npscal=0 is the default in Amber (uniform coordinate scaling).

ndfmin =0 (default) is recommended, unless you are performing a
belly run, etc. See p.167 in Amber 7 manual.

Rhonda

Rhonda A. Torres
The Scripps Research Institute
Department of Molecular Biology
10550 N. Torrey Pines Rd. TPC 15
La Jolla, CA 92037

email: torres_at_scripps.edu
phone: (858) 784-9781
fax: (858) 784-8896
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