VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Dec 13 2008 - 16:37:11 CST

On Sat, 13 Dec 2008, Lan Hua wrote:

LH> Hi,
LH>
LH> I have a simple question about the definition of the keyword "radius" of
LH> the atom selection.

LH> I thought the value I obtained using $sel get {radius} was van der Waals
LH> radius, but it seems not consistent with what I calculated by r0/2^(1/6)
LH> where r0 is from parm99.dat. So does the keyword "radius" mean van der Waals
LH> radius? Thank you in advance.

please note that van der waals radii are not the sigma
values from lennard-jones interactions.

radius values are - when supported - taken from the provided
coordinate file (e.g. for PQR format files) or a from table
with the following properties.

/*
 * corresponding table of VDW radii.
 * van der Waals radii are taken from A. Bondi,
 * J. Phys. Chem., 68, 441 - 452, 1964,
 * except the value for H, which is taken from R.S. Rowland & R. Taylor,
 * J.Phys.Chem., 100, 7384 - 7391, 1996. Radii that are not available in
 * either of these publications have RvdW = 2.00 <C5>.
 * The radii for Ions (Na, K, Cl, Ca, Mg, and Cs are based on the CHARMM27
 * Rmin/2 parameters for (SOD, POT, CLA, CAL, MG, CES) by default.
 */

cheers,
   axel.

LH>
LH>
LH> Best,
LH>
LH> Lan
LH> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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