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#448 10/24/03 06:49 AM
Joined: Oct 2003
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tjaart Offline OP
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I got the following parameters from a CHARMM input script and would like to know if anyone can tell me what SWITch means and what good values are for CTONnb and CTOFnb?

NBONd CUTNb 15.0 CTONnb 14.0 CTOFnb 14.5 SWITch VSWItch -
CDIElectric EPSilon 4.0

CHARMM always gives warnings that these two are too close.
Is CDIElectric EPSilon the dielectric constant of the environment (e.g. 1 for vacumm and 80 for water)?


Tjaart de Beer
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SWITch specifies that the truncation of the electrostatic interaction should be handled by a smooth change of Ecoulomb from CTONNB to CTOFNB, which in your case is a 0.5A interval. This is not a good idea because over that short interval the energy will vary rapidly, leading to a large, artificial force at a fairly long distance.
See nbonds.doc:


[ ATOM ] [ CDIElec ] [ SWITched ] NO! Very bad - do not use!
For a better description of these methods and how they perform, see:
P.J. Steinbach, B.R. Brooks: "New Spherical-Cutoff Methods for Long-Range
Forces in Macromolecular Simulation," J. Comp. Chem. 15, 667-683 (1994)."
See also Norberg, J., and Nilsson, L. (2000). On the Truncation of Long-Range Electrostatic Interactions in DNA. Biophysical Journal 79, 1537-1553.

EPSilon is the dielectric constant used in Coulomb's law to evaluate pairwise electrostatic interactions, and it should be 1 for explicit solvent simulations.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  BRBrooks, lennart, rmv 

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