Thanks.
So from your suggestion of the harmonic strength, do you mean that on each
coordinate, the harmonic constant would be about 10/9000 kcal/mol*A^2 (as
there are 9000 cv_r ) to calculate force ? In that case I do need to have a
large harm value to pull the atoms. (Yes, the harm=10 seems not pull the
atoms in the trajectory.)
Also, I have question on the path and harm settings. If I have 5 values
(elements) in the path variable, and the simulation is 1000 steps. Does
that mean that the elements for the cv in the simulation would be set
evenly among the time steps, with 1st value at step=0, 2nd value at
step=250, 3rd value at step=500 ... 5th value at step=1000?
Xiaoling Leng
Feng Pan <fpan3.ncsu.edu> 于2018年10月25日周四 下午4:52写道：
> Hi, Xiaoling
>
> The new NFE cannot recognize X in path as initial , that is the problem.
> what I would suggest is to run a single one-step md first, get the initial
> value for the
> cv in the monitor file, and then set it as the initial.
>
> BTW, you set harmonic strength to 10 kcal/mol, this could not be strong
> enough
> to pull the structure to target, but you can try first and then see if you
> need change.
>
> Best
> Feng
>
> On Thu, Oct 25, 2018 at 3:44 PM Xiaoling Leng <lengxl916.gmail.com> wrote:
>
> > Thanks. I tried the method you suggested, however there are still give
> > error says "** NFE-Error ** : Cannot read &colvar namelist!"
> >
> > Basically, I want to target a protein to the target structure. So the cv
> is
> > the Multy_RMSD, the atoms are the Ca atoms for the protein, and the
> > coordinate of the target is the corresponding Ca atoms' xyz coordinate on
> > the target structure. I am trying only use linear change of target (so
> the
> > RMSD is from X to 0, in the number of steps of this run, correct?)
> >
> > I followed the format described in the manual section, and don't know why
> > it call this error.
> > Attached is the running script (step3.mdin) and cv.in for colvar
> > definition.
> >
> >
> >
> >
> > Feng Pan <fpan3.ncsu.edu> 于2018年10月24日周三 下午2:06写道：
> >
> > > 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
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
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> > > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Feng Pan
> > > > > PostDoc
> > > > > North Carolina State University
> > > > > Department of Physics
> > > > > Email: fpan3.ncsu.edu
> > > > > _______________________________________________
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> > > > > 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
> > > _______________________________________________
> > > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Oct 26 2018 - 14:00:02 PDT
