AMBER Archive (2003)

Subject: Re: AMBER: slow simulation

From: David A. Case (case_at_scripps.edu)
Date: Mon Sep 22 2003 - 09:54:46 CDT

On Sun, Sep 21, 2003, nie beining wrote:

> I ran 200ps MD simulation with protein fixed to equilibrate water
> molecules. I found that coordinates were printed out 3ps/hr after I
> used the restart coordinates to run simulation allowing everything to
> move. The simulation without equilibrating water was printing
> coordinates at 7ps/hr. I am a pretty new user. Is there any reason for
> slower printing out? How to improve the speed of simulation without
> changing any control parameters? Thanks!
>

We would need more information: which version of sander? how big is the
system? how were you holding the protein fixed? You might be able to compare
your timings to those on the Amber benchmark page, to kind of see what you
should expect.

..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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