Re: [AMBER] Minimization Time Limit Error with Sander

From: David A Case <david.case.rutgers.edu>
Date: Fri, 18 Dec 2020 17:10:57 -0500

On Fri, Dec 18, 2020, Aanshi Gandhi wrote:

[minimization is taking too long]:

My usual prescription for debugging: try a short run first to make sure
things are working.

You are asking for 100000 minimization steps, which is probably way too
many. You also set ncyc to 10000, which means that you are only using
steepest descent (which is very inefficient) for way too long.

Try this: set maxcyc=1000, ncyc=50, ntpr=50. That run should finish
within your time limit, and you can determine how long each step is
taking. If you feel you need more minimization, you and start from
where the first run left off, and go further.

....good luck....dac


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Received on Fri Dec 18 2020 - 14:30:02 PST
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