On Sat, Nov 26, 2011, Yun Shi wrote:
>
> I wonder, if I could implement different cutoff values for VDW and
> electrostatic interactions (i.e. in GROMACS), would that be theoretically
> better to use 9 angstroms for electrostatic cutoff and 14 angstroms for the
> VDW?
Yes, it would theoretically be better. Van der Waals interactions beyond the
cutoff are estimated from a continuum model, which works best for nearly
isotropic systems. If you have structures that are very different in one
direction than another, you might want to play around with using a longer
cutoff for vdW interactions than for electrostatics. This is easy to do in
the cpu version of pmemd; not yet implemented (as far as I know) in the cuda
version.
....dac
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Received on Mon Nov 28 2011 - 07:00:03 PST
