Hi,
Check section 21.6.4 in the manual for the usage of &pmd, also there are
some examples of input
there. Check section 21.6.2 for the format of collective variables, the
COM_ANGLE and COM_TORSION
should be helpful to you
Best
Feng
On Tue, Mar 20, 2018 at 9:34 PM, Rajarshi Roy <phd1701171011.iiti.ac.in>
wrote:
> 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 [Please, someone correct me if I'm wrong, or out of date here!]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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> > >
> > >
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> >
> >
> >
> > --
> > Feng Pan
> > Ph.D.
> > North Carolina State University
> > Department of Physics
> > Email: fpan3.ncsu.edu
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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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 - 19:00:03 PDT
