AMBER Archive (2005)

Subject: Re: AMBER: STARTING WHERE I LEFT OFF

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Sat Sep 03 2005 - 12:58:29 CDT

you can also use ptraj to extract the last frame of the trajectory
to a restart format and just reinitialize the velocities using either the
forces or a random number.

Bill Ross wrote:

>>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
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu