AMBER Archive (2003)

Subject: Re: water reordering in sander

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 07 2003 - 10:03:58 CST

On Tue, Jan 07, 2003, Michael Trieb wrote:

> - What is the main function of the "water reordering process" ?

It speeds up parallel calculations, by a significant amount but not by a
lot.

> - What consequences will this have on the md-calculations and what is
> the connection between nmropt, PME and water reordering?

There will be no consequences for the output, just for the time it takes to
get there. If you don't have either weight changes or restraints (as your
sample input indicates) I would recommend setting nmropt=0.

..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
==================================================================