Dear Sir,
Yes sir. I added infe=1 and &cntrl in my script. I think as I am doing
normal umbrella sampling, may be that is the reason for that.
On Tue, Mar 27, 2018 at 1:05 AM, Feng Pan <fpan3.ncsu.edu> wrote:
> 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
> _______________________________________________
> 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 Apr 03 2018 - 23:30:02 PDT
