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
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Received on Wed Mar 21 2018 - 05:00:02 PDT
