Perhaps it would help if you explained why you want to do these things. I
can't readily imagine why you would want to freeze your protein in that way
in an implicit solvent simulation.
In terms of part 2, do you mean that you want a periodic box? Or do you
mean that you want to restrain the ligand to only ever move a certain
distance from your protein?
On Fri, Feb 17, 2012 at 7:52 AM, Jason Swails <jason.swails.gmail.com>wrote:
> It completely depends on what you're trying to do.
>
> Without that it's hard to give anything but the most generic (unhelpful)
> advice.
>
> Think hard about the question you are trying to answer and what simulation
> details would be required to probe that.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Feb 17, 2012, at 1:21 AM, Danny Xu <quantum_mania.yahoo.com> wrote:
>
> > Hello,
> >
> > In an igb simulation, what would be a good approach to:
> >
> > 1. restrain the protein to remove its rotation/translation, in another
> word, fix its center of mass
> > 2. confine a ligand to move only inside a defined 3D box
> >
> > Thanks very much in advance!
> >
> > -DX
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Fri Feb 17 2012 - 05:30:02 PST
