The following paper might be of interest:
Shirts, *et al. *Accurate and Efficient Corrections for Missing Dispersion
Interactions in Molecular
Simulations, *J. Phys. Chem. B* *2007, **111*, 13052-13063.
Regards,
Brian
On Fri, Dec 6, 2013 at 2:22 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, Dec 06, 2013, yunshi11 . wrote:
> >
> > 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?
>
> Yes.
>
> >
> >
> > 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?
>
> This is certainly true. There have been many publications on the
> sensitivity
> (sometimes rather extreme) of bilayer simulations to the LJ cutoff.
>
> >
> > 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
> > simulation?
>
> I don't recall seeing any tests of this issue; perhaps others can chime in.
> If you are already (artifically) steering your trajectory, it may be hard
> to
> predict the effects of a bias in how long-range LJ interactions are
> handled.
>
> >
> > Generally speaking, if one has enough computational resources, would it
> > always be safer to use a large cutoff distance for vdW interactions?
>
> Well, a large cutoff implies a large box and a slower-running simulation.
> In most cases, this in practice leads to less sampling (e.g. through a
> shorter
> simulation). These sorts of trade-offs depend a lot on what you are
> trying to
> learn.
>
> ...dac
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Fri Dec 06 2013 - 12:30:03 PST
