AMBER Archive (2005)

Subject: Re: AMBER: STARTING WHERE I LEFT OFF

From: Claire Zerafa (cporteli_at_waldonet.net.mt)
Date: Sat Sep 03 2005 - 12:49:31 CDT

THANK YOU!!
----- Original Message -----
From: "Bill Ross" <ross_at_cgl.ucsf.edu>
To: <amber_at_scripps.edu>
Sent: Saturday, September 03, 2005 7:36 PM
Subject: Re: AMBER: STARTING WHERE I LEFT OFF

>> i have set 6 dynamics runs
>> simultaneously and am running out of HD space. How can I carry on where
>> the
>> dynamics left off if the run stalls?
>
> You can only restart from a restrt file that includes coordinates
> and velocities at the timestep it was saved. If you aren't saving
> these at regular intervals, you will have to start over.
>
> The only exception is if you are saving mdvel as well as mdcrd, you
> can synthesize a restrt by extracting the corresponding frame from
> each, convert to the correct format, and manually merging to make
> a restrt. This restrt would have less precision than a real restrt
> (just as a real ascii restrt has less precision than a binary one),
> so the trajectory will be somewhat different. However I don't know
> of any general worries about this sort of issue.
>
> Bill
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