Is there no way you can renumber the atoms to facilitate grouping?
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-----Original Message-----
From: Ignacio General <ijgeneral.gmail.com>
Sent: Monday, April 20, 2020 2:06 PM
To: amber.ambermd.org
Subject: [AMBER] restraining many individual atoms
Dear Amber users,
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, so this is not good enough.
I thought of using the old group specification but, again, since the atoms
are not ordered, I need to create a group for each atom. In that case, I
will need to have a sequence of several hundred groups, something like this:
Group 1:
10.0
ATOM 265
END
Group 2:
10.0
ATOM 267
END
...
Group 200:
10.0
ATOM 5215
END
END
Anybody can think of a better way of doing this? And if I do it this way, is
there a limit to the number of groups that can be given to pmemd.cuda?
Thanks for your help,
Ignacio
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Received on Mon Apr 20 2020 - 13:00:02 PDT
