Re: [AMBER] restraining many individual atoms

From: James Kress <jimkress_58.kressworks.org>
Date: Mon, 20 Apr 2020 15:37:44 -0400

Is there no way you can renumber the atoms to facilitate grouping?

James Kress Ph.D., President
The KressWorksR Institute
An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
"ENGINEERING THE CURE" C
(248) 573-5499

Learn More and Donate At:
Website: http://www.kressworks.org
Facebook: https://www.facebook.com/KressWorks.Institute/

Confidentiality Notice | This e-mail message, including any attachments, is
for the sole use of the intended recipient(s) and may contain confidential
or proprietary information. Any unauthorized review, use, disclosure or
distribution is prohibited. If you are not the intended recipient,
immediately contact the sender by reply e-mail and destroy all copies of the
original message.

-----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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 20 2020 - 13:00:02 PDT
Custom Search