Re: [AMBER] About generalized restraints in AMBER14 with GPU support

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 24 Mar 2015 10:48:46 -0400

On Tue, Mar 24, 2015 at 10:29 AM, Attilio Vittorio Vargiu <
vargiu.dsf.unica.it> wrote:

> Dear Amber community,
> sorry if this topic has been already posted. Before writing I checked
> extensively the mailing list and it seems this option is not active yet,
> but I was wondering if there was some last minute news concerning this
> point, even at the level of developing codes.
> Namely, I was wondering if there is any way in AMBER14 of using a
> generalized restraint (namely restraining the difference between two
> distances, each involving centers of mass of groups of atoms) using pmemd
> in place of sander.
> I have seen that the distance between centers of mass has been implemented
> (
> http://ambermd.org/bugfixes/14.0/update.10), but as far as I can see from
> the manuals, there is no way of implementing such generalized coordinates
> by using the GPU version of the code.
> I understood that with the "old" syntax one should use something like the
> following example, which indeed seems to work properly for my system (or
> better, sander runs...):
>

‚ÄčNo. It is not even implemented in the CPU pmemd version, let alone
pmemd.cuda. It is probably on the list of things to do, but there is no
timetable for its addition to my knowledge (other things are ahead in the
priority list, I think).

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 24 2015 - 08:00:02 PDT
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