AMBER Archive (2002)

Subject: Re: restart md simulation

From: Michael G Cooney (chemgc_at_panther.Gsu.EDU)
Date: Tue Jan 29 2002 - 10:44:03 CST

Dear Dr. Richter:

I don't know of any option in Amber 5 to add to existing output files, but
you can merge two or more coordinate files using ptraj (rdparm) or carnal.
The manuals should tell how to do this. If restarting MD (irest=1), the
input coordinate file (-c option in the sander command line) should be the
last restart file, not the large mdcrd file which contains the whole
trajectory. Hope this helps.

Sincerely,

Michael Cooney
Dept. of Chemistry
Georgia State University
Atlanta, GA 30303, USA

On Tue, 29 Jan 2002, Uwe Richter wrote:

> Dear Amber users,
>
> is there a special option in Amber that tells the program
> to restart a MD simulation and to add the output to the
> existing files (mdcrd, mden etc.). Or do I just have to
> take the last written .crd file and start over. In the
> latter case, whats the best way to merge the two pieces
> of the long simulation afterwards.
>
> Thanks,
> Uwe
>
>