I could do it one time, but the idea is to apply this to many different
systems, so I think its not a good idea. I mean, I can do it if there is no
other option, but would rather find an option. Thanks!
On Mon, Apr 20, 2020 at 4:38 PM James Kress <jimkress_58.kressworks.org>
wrote:
> 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
