[AMBER] Should vdW cutoff distance be system-dependent?

From: yunshi11 . <yunshi09.gmail.com>
Date: Fri, 6 Dec 2013 09:38:28 -0800

Hi everyone,

I understand that AMBER implements (by default) a continuum model to
correct energy and pressure for vdW interactions beyond the cutoff (e.g. 8
or 10 angstroms). Does this model simply correct for the r^-6 term that is
responsible for LJ attractions?

It also seems to me that such a model assumes an isotropic environment
beyond the cutoff distance, which is not necessarily true for all
bio-molecular systems. If one has a large and strangely shaped protein or a
lipid bi-layer to model, should a much larger cutoff distance be used?

I wonder if this would also, in theory, affect results for steered MD
simulations that pulls a ligand away from a protein. When the ligand is,
say, 8 angstroms from its binding site, it is not in an isotropic
environment, with one side being amino acid residues and the other being
waters. Should a larger cut (e.g. 15 angstroms) be applied for this kind of

Generally speaking, if one has enough computational resources, would it
always be safer to use a large cutoff distance for vdW interactions?

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Received on Fri Dec 06 2013 - 10:00:02 PST
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