Re: reassigning temp. during MD

From: Robert Matthew Fesinmeyer <>
Date: Mon 21 Aug 2000 15:20:53 -0700 (PDT)

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

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?


R. M. Fesinmeyer
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
Received on Mon Aug 21 2000 - 15:20:53 PDT
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