Re: [AMBER] restraining many individual atoms

From: David A Case <>
Date: Mon, 20 Apr 2020 15:55:38 -0400

On Mon, Apr 20, 2020, Ignacio General wrote:
>I need to do some MD runs with pmemd.cuda, restraining the position of
>several hundred atoms. The problem is that they are not sequential, so that
>I can't use ranges of values, but have to list them individually. ntr=1
>with restraintmask only allows 256 characters,

It's certainly worth a try to just edit mdin_ctrl_dat.F90 (in
$AMBERHOME/src/pmemd/src), and change the size of restrainmask to
something like 3000, or whatever you need. You will also need to
edit findmask.F90, and change BUFLEN to the same value.

You clearly would need to run some tests to make sure nothing bad is


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Received on Mon Apr 20 2020 - 13:00:03 PDT
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