AMBER Archive (2004)

Subject: Re: AMBER: Trouble running molecular dynamics with an increase in temp in Sander

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 16 2004 - 09:40:32 CDT

On Wed, Jun 16, 2004, Robyn Ayscue wrote:

> Hi! I've been trying to run a molecular dynamics
> simulation (using Sander in Amber 8) on a solvated
> (TIP3/Na+), modified DNA 15-mer (holding the DNA
> fixed), and after about twenty minutes or so the
> program dies. In the .out file I keep getting several
> vlimit errors, and the temperature seems to be
> increasing exponentially until it reaches some
> astronomical number and blows up.

Three things to try:

1. You may well need to minimize your intitial structure before running MD.

2. You must equilibrate first at constant volume before turning on constant
pressure.

3. Reduce the force constants for your restrained atoms from 500 to about 5
kcal/mol-Ang**2.

...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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