Hello, Ramin
For NFE you can do distance only in X Y or Z direction, but you need to
write the codes
for the new variable in the source code and recompile,
here is an example I put in tutorial, which the distance in Z distance, it
may help you if you want to try
http://ambermd.org/tutorials/advanced/tutorial31/custom_cv/index.html
Best
Feng
On Wed, Sep 23, 2020 at 9:56 AM Ramin Mehrani <raminmehrani88.gmail.com>
wrote:
> Thank you David and Feng. I did not know about the NFE options. I went
> through it and I found it a great option for biasing the simulation with
> harmonic potential. However, I think it has the downside on COM_distance
> that we can not control the distance in the X or Y or Z directions. This
> means that it requires the larger simulation box to satisfy the
> periodic boundary conditions. I would appreciate it if you have any
> suggestion on this problem.
>
> On Tue, Sep 22, 2020 at 3:45 PM Feng Pan <fpan3.ncsu.edu> wrote:
>
> > If you use the COM_DISTANCE variable in NFE module, you can
> > use up to 20000 atoms. You can set to an even higher number if you do
> easy
> > change in
> > the source code. As David said, you can look into Section 23.4 in the
> > Reference Manual
> > for the usage.
> >
> > Best
> > Feng Pan
> >
> > On Tue, Sep 22, 2020 at 11:22 AM David A Case <david.case.rutgers.edu>
> > wrote:
> >
> > > On Tue, Sep 22, 2020, Ramin Mehrani wrote:
> > > >
> > > >I am trying to do an umbrella sampling simulation with amber to
> > calculate
> > > >the dimerization free energy of protein with more than 200 residues.
> The
> > > >major part of this calculation is to apply a harmonic restraint to the
> > > >distance between two proteins chain. The harmonic restraint will keep
> > the
> > > >distance fluctuating around a target distance with tunable amplitude.
> > >
> > > >According to this tutorial, to apply the harmonic restraint to the
> > > distance
> > > >we need to define the center of mass of two groups of atoms via "igr1
> > and
> > > >igr2". The problem with this method is that we cannot group more than
> > 200
> > > >atoms. I was wondering if you know a method in amber that I can apply
> > the
> > > >harmonic restraint to the distance between two groups with more than
> 200
> > > >atoms. I am asking this because each protein chain in my study has
> more
> > > >than 200 atoms.
> > >
> > > Simplest approach is to choose a subset of atoms, say the CA atoms in
> > > residues in regular secondary structure. Use the center of mass of
> > > those atoms as a surrogate for the COM of the whole protein.
> > >
> > > I'm not sure if the "nfe" collective variables let you define groups
> > > with an arbitrary number of atoms or not. You might look into that
> > > options as well (Section 23.4 in the Reference Manual.)
> > >
> > > ...dac
> > >
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > Feng Pan
> > PostDoc
> > Florida State University
> > Department of Statistics
> > Email: fpan3.ncsu.edu; fpan.fsu.edu
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
PostDoc
Florida State University
Department of Statistics
Email: fpan3.ncsu.edu; fpan.fsu.edu
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Received on Fri Sep 25 2020 - 07:00:03 PDT
