AMBER Archive (2004)

Subject: Re: AMBER: Vlimit problem

From: David A. Case (case_at_scripps.edu)
Date: Thu Jan 08 2004 - 18:31:00 CST

You wrote:

> I have encountered a problem with vlimit when runing the simulation of an
> unmodified control of a 11mer B - DNA with 20 Na+ counterions added and
> waterbox of 10 A in each dimension. I set vlimit=15.0 for the second step
> "dynamics holding the solute fixed",after 1000 steps of steepest descent
> minimization and 4000 steps of conjugate gradient minimization.

You have to heat the system to the final temperature (say 300K) at constant
volume *before* you turn on constant pressure.

Also, please send email to the list as plain text, not as html.

..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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