AMBER Archive (2000)

Subject: Re: reassigning temp. during MD

From: Robert Matthew Fesinmeyer (rmf_at_u.washington.edu)
Date: Mon Aug 21 2000 - 17:20:53 CDT

I noticed this question went unanswered. I believe that the way you do
this is to use the NRUN variable in combination with the NSTLIM and DT
variables. Thus instead of running one 1ns run (NRUN=1, and
DT*NSTLIM=1ns), you'd set NRUN=2 and DT*NSTLIM=500ps. I believe this
would allow the run to go for 1ns, but would reassign the velocities after
500ps.

I hope that someone will confirm or deny this statement.

As a sidenote, is there a consensus opinion to the reassignment of
velocities for a problematic system? Is once per 200ps generally thought
of as valid, but not, say, once per 10ps?

Thanks,
Matt

_________________________
R. M. Fesinmeyer
rmf_at_u.washington.edu
Department of Chemistry
University of Washington

On Fri, 11 Aug 2000, Raik Gruenberg wrote:

> Hi,
>
> is it possible to prompt sander to reassign velocities from a Maxwell
> distribution such and such often in the course of a MD run?
> I faced some difficulties to equilibrate my protein and the only
> work-around I have come up with so far is to restart the simulation
> several times.
>
> Thanks for any advise
> and have a nice weekend!
>
> Ciao
> Raik
> ____________________________
> Raik Gruenberg
> gruenber_at_embl-heidelberg.de
> www.raiks.de/contact.html
>
>