Hi
Thank you for the information. Can you please tell me how to use & pmd
module. I never use this one.
On 21 Mar 2018 3:19 am, "Feng Pan" <fpan3.ncsu.edu> wrote:
> 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 [Please, someone correct me if I'm wrong, or out of date here!]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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>
>
> --
> 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 - 19:00:02 PDT
