Re: [AMBER] About restraint

From: Aron Broom <>
Date: Tue, 17 Apr 2012 22:47:06 -0400

I'm not sure to what extent that is possible without making the simulation
meaningless. The intramolecular forces for your "big" molecule are almost
certainly critical for it's structure, and it doesn't have just 1 single
structure, but an ensemble of structures that will contribute differently
to the interaction with your "small" molecule, and thus must be
considered. That being said, if you really want to continue, I think you
can fix the positions of certain atoms, using a restraint mask (or
something like that) and thereby not have to calculate those interactions.

If you are doing PME with periodic boundary conditions, the electrostatic
cutoff will already help you by not calculating the direct electrostatic
interactions between distant parts of your large molecule.

Are you using explicit solvent? Perhaps it is possible to include the
solvent only inside your "big" molecule and thus save time calculating the
external solvent, although this could also lead to problems.

What is this big molecule, some kind of giant fullerene?

On Tue, Apr 17, 2012 at 10:33 PM, Jun Wang <> wrote:

> Dear amber users,
> I'm using amber11 to do MD simulation on a system which contains a very
> huge molecular and a peptide inside it. In order to accelerate the
> simulation. I want to constrain the big molecular without calculating its
> inner interaction. That is to say, I just want to treat the big molecular
> as the environment and only calculate the energy between the small peptide
> and environment. I don't know how to write the input file of my simulation.
> Any help would be appreciated!
> Regards!
> Jun
> _______________________________________________
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Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
AMBER mailing list
Received on Tue Apr 17 2012 - 20:00:05 PDT
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