Re: [AMBER] restraining many individual atoms

From: Ignacio J. General <>
Date: Mon, 20 Apr 2020 17:31:21 -0300

Ok, I will try that. Thanks for the advice!

And by the way, do you know why a length of 256 was chosen for
restraintmask? Was there a reason for that, or just random choice? I ask
just to make sure I don't break anything else, but of course, I will run
some test to make sure things stay reasonable.


On Mon, Apr 20, 2020 at 4:55 PM David A Case <> wrote:

> 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
> happening.
> ....dac
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Received on Mon Apr 20 2020 - 14:00:02 PDT
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