Thank you for your help. I will try to do that.
On Wed, Mar 21, 2018 at 9:11 AM, Feng Pan <fpan3.ncsu.edu> wrote:
> You can use &pmd in cuda now when you update Amber16 to latest version.
>
> Feng
>
> On Tue, Mar 20, 2018 at 11:39 PM, Rajarshi Roy <phd1701171011.iiti.ac.in>
> wrote:
>
> > Hi,
> >
> > Thank you for your help. But &pmd is only for sander , but I want you to
> > run the umbralla sampling in cuda.
> >
> > On Wed, Mar 21, 2018 at 7:14 AM, Feng Pan <fpan3.ncsu.edu> wrote:
> >
> > > 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
> > > > > > >>
> > > > > > >>
> > > > > > >> _______________________________________________
> > > > > > >> AMBER mailing list
> > > > > > >> AMBER.ambermd.org
> > > > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >>
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > >
> > > > > > > with regards
> > > > > > > Rajarshi Roy
> > > > > > >
> > > > > > > PhD Research Scholar
> > > > > > > Biosciences and Biomedical Engineering
> > > > > > > Indian Institute of Technology, Indore
> > > > > > > India
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > >
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Feng Pan
> > > > > Ph.D.
> > > > > North Carolina State University
> > > > > Department of Physics
> > > > > Email: fpan3.ncsu.edu
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Feng Pan
> > > Ph.D.
> > > North Carolina State University
> > > Department of Physics
> > > Email: fpan3.ncsu.edu
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> >
> > with regards
> > Rajarshi Roy
> >
> > PhD Research Scholar
> > Biosciences and Biomedical Engineering
> > Indian Institute of Technology, Indore
> > India
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Feng Pan
> Ph.D.
> North Carolina State University
> Department of Physics
> Email: fpan3.ncsu.edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
with regards
Rajarshi Roy
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
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Received on Tue Mar 20 2018 - 21:00:04 PDT
