Re: [AMBER] Restarting PMEMD calculation after server shutdown

From: David A Case <>
Date: Thu, 2 Aug 2012 08:05:01 -0400

On Thu, Aug 02, 2012, Saaz Sakrikar wrote:

> I have faced a recurring problem when trying to do a pmemd simulation on my
> server. It is a long calculation (nstlim = 15 million)
> The server has many shutdowns and thrice the calculation has been stopped
> in the middle of the run. Is it possible to resart it from where it left
> off and not from scratch? Or is that only for Sander calculations?
> I have saved mdcrd and rst files from these attempts.

You can start with any rst file that was correctly written, but it is likely
to be a bit (or a lot) of a pain to combine all the mdcrd files if jobs were
stopped in the middle.

I rarely (=never) try to run really long calculations in a single run, but
rather plan in advance to split things into bite-size pieces, no more than
24-48 hours each. That way, if the server fails, you lose at most 1-2 days.
Depending on how you access the server, you may be able to create a simple
script that will automatically submit a second job when the first one is

...good luck....dac

AMBER mailing list
Received on Thu Aug 02 2012 - 05:30:04 PDT
Custom Search