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 

-- 

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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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