Yes, that's right.
Feng
On Wed, Oct 24, 2018 at 10:55 AM Xiaoling Leng <lengxl916.gmail.com> wrote:
> Hello Feng
>
> Thank you very much.
> As I look through 21.6.2, it seems the MULTI_RMSD type for reaction
> coordinate is the best mimic for RMSD restraint in targeted MD.
> Am I correct?
>
> Thanks.
>
> Xiaoling Leng
>
> Feng Pan <fpan3.ncsu.edu> 于2018年10月18日周四 下午6:18写道：
>
> > Hi, Xiaoling
> >
> > You may try the SMD method in NFE module, with the use of RMSD as the
> > reaction coordinates
> >
> > for the details of this usage, you can check the manual section 21.6.3
> for
> > the usage of &smd,
> > and 21.6.2 for the RMSD reaction coordinate
> >
> > Feng
> >
> > On Thu, Oct 18, 2018 at 2:54 PM Xiaoling Leng <lengxl916.gmail.com>
> wrote:
> >
> > > Hello,
> > >
> > > I want to perform a targeted MD simulation on a membrane protein.
> However
> > > it is not supported in the pmemd GPU version. May I ask is there any
> > > alternative way for doing it using GPU? Or like what other types of
> > > restraints is available in the pmemd can help to simulate a transition
> in
> > > between structures?
> > >
> > > Thanks.
> > >
> > > Xiaoling Leng
> > > _______________________________________________
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> > >
> >
> >
> > --
> > Feng Pan
> > PostDoc
> > North Carolina State University
> > Department of Physics
> > Email: fpan3.ncsu.edu
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Feng Pan
PostDoc
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Wed Oct 24 2018 - 11:30:01 PDT
