AMBER Archive (2009)

Subject: Re: [AMBER] LJ parameters for HO and HW

Date: Mon Nov 09 2009 - 02:23:20 CST


I believe the idea of having 0.0 vdw radius hydrogens is to speed up the
vdw calculation (only 1/9 of interactions in a system consisting mostly of
water) by making the small hydrogens vdw-less charge points.

It is assumed (and normally true) that the vdw radius of nearby oxygens is
enough to keep other particles from crashing into the hydrogens. The
oxygen radius of OW was slightly increased during parameter generation
(see parm99.dat, OW is the biggest oxygen type there is) to compensate for
this. So water molecules like TIP3P are spherical in terms of

Kind Regards,

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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