Hi,
Have you added infe=1 to &cntrl namelist in mdin file?
Feng
On Wed, Mar 21, 2018 at 7:41 AM, Rajarshi Roy <phd1701171011.iiti.ac.in>
wrote:
> Dear Sir,
>
> I have a query about &pmd. Is &pmd only for restraining REMD coupled
> umbrella sampling ? I am trying to run normal umbrella sampling. Now I
> changed my script &rst to &pmd and also it is running in cuda. But now the
> values of restraint co-ordinate is not generating.
>
> On Wed, Mar 21, 2018 at 9:24 AM, Rajarshi Roy <phd1701171011.iiti.ac.in>
> wrote:
>
> > 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
> >
>
>
>
> --
>
> 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
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Received on Mon Mar 26 2018 - 13:00:03 PDT
