# Re: [AMBER] Alternative way to do targeted MD

From: Feng Pan <fpan3.ncsu.edu>
Date: Sun, 28 Oct 2018 15:41:07 -0400

Hi, Xiaoling

Yes, it is not simply numerical average for each atom, but basically when
the number of
atom goes high, we always need high value of harmonic strength. I would
suggest you
try some large numbers like 100, 500 kcal/mol, check the trajectory,
monitor file to
see what happens

For the path and harm type, the default is SPLINE, so if you want a linear
increasing,
just set parm_mode or harm_mode to 'LINES', this is also explained in the
manual

Best
Feng

On Fri, Oct 26, 2018 at 4:49 PM Xiaoling Leng <lengxl916.gmail.com> wrote:

> 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
> > > > > > > AMBER.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Feng Pan
> > > > > > PostDoc
> > > > > > North Carolina State University
> > > > > > Department of Physics
> > > > > > Email: fpan3.ncsu.edu
> > > > > > _______________________________________________
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> > > > > > 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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> > > >
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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
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Received on Sun Oct 28 2018 - 13:00:02 PDT
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