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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>
--
Feng Pan
PostDoc
Florida State University
Department of Statistics
Email: fpan3.ncsu.edu; fpan.fsu.edu
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Received on Tue Sep 22 2020 - 13:00:02 PDT
