Re: [AMBER] nmode entropy calculations gets stuck way too often

From: David A Case <>
Date: Sat, 4 Apr 2020 13:30:24 -0400

On Fri, Apr 03, 2020, Liao wrote:
>With drms=0.002, maxcyc=1000, I can see that in the nm.out file that gets
>stuck (usually stuck already by 200ns), the RMSG will go back and forth
>between a certain value, and never reach the drms value set. Whether
>maxcyc=1000 or 10000 doesn’t help, it usually gets stuck by iteration 200
>or so.

This is a case where you may need to do the entropy part "by hand". I'd
explore using txmin.c to carry out the minimization, and tnmode.c to do
the subsequent normal mode analysis. (These programs are in
AmberTools/test/nabc; you can also use NAB versions of the same thing.)
Be sure you have SHAKE turned off in the minimization.

Equally well, you can modify the sander minimization to use xmin (set

Caveat: I'm not familiar with how many options you have in using the scripts -- there may be option there that others on the list
can suggest.

It would help to know how big your system is.


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Received on Sat Apr 04 2020 - 11:00:02 PDT
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