Re: Restart MD from a certain point?

From: Axel Kohlmeyer (
Date: Thu Oct 14 2010 - 09:04:49 CDT

dear wendy,

2010/10/14 Wendy González <>:
> Dear NAMD users:
> I have a MD simulation of 2040000 steps and I would like to restart it from
> step 700000 applying some constraints. How can I do it?

well, ideally by restarting from a restart. you did write out and saved
periodic restarts like it is common good practice, or didn't you?

> I tried to give as initial coordinate the step 700000 (see below) but it did
> not work. Should I add other parameter?

please explain _how_ it "did not work"?

it is impossible to give advice without knowing what
has happened and what you did exactly.


> structure           ionized.psf
> coordinates         step_700000.pdb
> binvelocities       DM_5ns.restart.vel
> extendedSystem      DM_5ns.restart.xsc

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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