Hi, Rajarshi
You can use angle and dihedral COM restraints by the &pmd module.
Best
Feng
On Tue, Mar 20, 2018 at 11:15 AM, Rajarshi Roy <phd1701171011.iiti.ac.in>
wrote:
> Ok thank you
>
> On 20 Mar 2018 8:16 pm, "Ross Walker" <ross.rosswalker.co.uk> wrote:
>
> Hi Rajarshi,
>
> Dave is correct the GPU code only supports distance based center of mass
> restraints. Angle and dihedral COM restraints are not supported.
>
> The only option right now is to use the CPU code.
>
> All the best
> Ross
>
> > On Mar 19, 2018, at 06:39, Rajarshi Roy <phd1701171011.iiti.ac.in>
> wrote:
> >
> > 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 <david.case.rutgers.edu>
> > wrote:
> >
> >> 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 [Please, someone correct me if I'm wrong, or out of date here!]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
> > India
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>
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--
Feng Pan
Ph.D.
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Tue Mar 20 2018 - 15:00:02 PDT
