AMBER Archive (2003)

Subject: Re: AMBER: Implicit MD simulations in Amber7

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Mon Oct 27 2003 - 14:20:14 CST

Hello,

You'll need to turn off PME;
ntb = 0
Use a large (16 Ang) or infinite nonbonded cutoff;
cut=16
Possibly evaluate the derivatives with respect to the effective
radii less frequently (this will improve computational efficiency):
nrespa=2 or 4

For further information google search the archives, eg,
cutoffs in GB site:structbio.vanderbilt.edu

Scott Brozell, Ph.D. | e-mail: sbrozell_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-8754
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/~sbrozell

On Mon, 27 Oct 2003, Joey Harriman wrote:

> Hi everyone,
>
> I am currently in the process of running some implicit MD simulations in Amber7. As
> far
> as I can tell the only flags that need to be included in the MD input file are:
> gbsa=1
> igb=1
> extdiel=***
>
> Can anyone confirm this? In addition, I am trying to do a MD simulation on a ligand in
> Toluene (extdiel=2.4)...are there any suggestions to make this calculation faster? I
> am currently usine SHAKE 2 for the calculations.
>
> Thanks in advance for your response,
> Joey Harriman
> ----------------------------------
> Joey Harriman
> MSc Computational Chemistry
> University of New Brunswick
> Room 228
> Toole Hall
> s808o_at_unb.ca
> 476-6543
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