Re: [AMBER] restart md simulation from different points

From: Jason Swails <>
Date: Thu, 16 Dec 2010 14:38:41 -0500

You can use ptraj to trajout restart files from any point along in the
simulation. It will automatically pull the box information for each step
from that frame in the trajectory (or at least it should, you can check

trajin trajectory.mdcrd 5 100 5
trajout snapshot.restrt restart

This will save the files snapshot.restrt.#, where # is 5, 10, 15, ..., 100.

If you've saved velocities, you can, in theory, extract velocities at the
same time steps and dump those into the restart files. However, this is a
little more difficult/involved since ptraj is not made to deal with mdvel
files, and they can only be netcdf-encoded.

You can, however, just have amber assign a random MB velocity distribution
at the start of the simulation.

Hope this helps,

On Thu, Dec 16, 2010 at 11:45 AM, Jorgen Simonsen <>wrote:

> Hi all,
> I want to restart my MD simulation using different points from an
> already production run - are there any script available for this in
> amber? I have been using periodic boundary conditions and I am not
> quite sure if I get them correctly by just exporting coordinates from
> VMD.
> Thx,
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Dec 16 2010 - 12:00:02 PST
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