Re: [AMBER] center of mass restraint in pmemd.cuda

From: Rajarshi Roy <>
Date: Mon, 19 Mar 2018 16:09:57 +0530

Dear Sir,
I make this restraint file using cpptraj. Is there any alternative way of
writing it or It is not possible to run in cuda?

On Mon, Mar 19, 2018 at 12:22 AM, David A Case <>

> On Thu, Mar 15, 2018, Rajarshi Roy wrote:
> >
> > I am trying do an umbrella sampling of nucleic acid. One of my restraint
> > co-ordinate is cpd angle (pseudo- dihedral angle ), for that I need to
> > restraint center of mass of four group of atoms. I am little bit confuse
> > how to choose the iat value. In the manual I found that it should be
> > negative, but it is not running in cuda. Here is my restraint file,
> I'm pretty sure pmemd.cuda only supports COM distance restraints, and
> not the corresponding angle or dihedral restraints.
> Hence the "igr3" and "igr4" namelist values are not legal ones.
> [Please, someone correct me if I'm wrong, or out of date here!]
> ....dac
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with regards
Rajarshi Roy
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
AMBER mailing list
Received on Mon Mar 19 2018 - 04:00:01 PDT
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