Re: [AMBER] How to set a check point in Amber

From: Dr. Anselm Horn <>
Date: Tue, 29 Jun 2021 10:20:45 +0200


I'm not aware of any such stop on a user condition; and to the best of
my knowledge there is also no possibility to stop a running simulation
(e.g. at the next rst-writing step) from 'outside' apart from killing
the job.
But the Amber experts and developers may correct me here.

A simple workaround:
Maybe you could set up an automatic chain job for your system with a run
time short enough for your purposes. Before resubmission, an analysis is
performed with cpptraj on the last subtrajectory to check for your break
condition. The job is then only resubmitted, if your distance criterion
is not fulfilled.

Maybe that helps.

Best regards,



On 06/28/2021 08:04 PM, Ramin Mehrani wrote:
> Hello,
> I was wondering if there is any way in Amber that we can automatically stop
> the simulation once the distance between two groups of atoms is below a
> certain threshold.
> Best,
> Ramin
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Tue Jun 29 2021 - 01:30:02 PDT
Custom Search