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
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Sep 23 2020 - 07:00:02 PDT
