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
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Received on Wed Oct 24 2018 - 08:00:02 PDT
