Re: [AMBER] Number of Cycles

From: Robert Duke <>
Date: Tue, 15 Dec 2009 12:54:28 -0500

If nstlim is evenly divisible by ntwx, then the last mdcrd trajectory frame
written should I believe correspond to the final restart file. The
important thing to remember, is that the restart file will always be written
at the final step of the run, regardless of the value of ntwr.
Regards - Bob Duke
----- Original Message -----
From: "Niel Henriksen" <>
To: "AMBER Mailing List" <>
Sent: Tuesday, December 15, 2009 12:41 PM
Subject: RE: [AMBER] Number of Cycles

Just a quick question regarding this thread . . .

Say i set ntwx=500 and let pmemd do its default
scaling for ntwr. Would I ever run ito a situation
where my trajectory file has frames written to it
that are later (in time) than the restart file. Thus
when i restart the job and create the next trajectory
file, I would essentially repeat the steps that have
already been calculated? And thus when I combine
all the frames in ptraj, I would have redundant data?

Thanks for the clarification,
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Received on Tue Dec 15 2009 - 10:00:05 PST
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