AMBER Archive (2003)Subject: Re: AMBER: vlimit?
From: David A. Case (case_at_scripps.edu)
Date: Fri Dec 26 2003 - 12:18:16 CST
On Tue, Dec 23, 2003, Ryan Ye wrote:
> I tried to use gradual warming and a larger value of
> taup but it still gave me similar results. This is one
> of the md_ntr.in files I tried:
You are only accepting pieces of the advice I gave before. You need
to heat to 300K or so at constant volume, _before_ going to constant
pressure. Always set irest=1 for every run after the very first one.
And, try reducing the force constant on your restraints (ntr=1) by about
two orders of magnitude.
..good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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