VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun Oct 26 2008 - 13:12:06 CDT

On Sun, 26 Oct 2008, wayj86 wayj86 wrote:

SW> Hi,all
SW>
SW> I am trying to use the namd energy plugin to analyze the tendency of
SW> interaction energy during the process of SMD.My question is:does the choice
SW> electrostatic energy(Elec) include the h-bond energy?If not,why not?Thank

stanley,
there is no explicit h-bond energy in the force field.
hydrogen bonds are simply a visual interpretation of
what results from the combination of the geometry of
molecules, charge distribution and pauli repulsion.

in typical classical MD force fields, this is modeled through
point charges _and_ the lennard-jones parameters.

cheers,
    axel.

SW> you very much for any help.
SW>
SW> Best wishes,
SW> Stanley
SW>
SW>
SW>
SW> 

-- 
=======================================================================
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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If you make something idiot-proof, the universe creates a better idiot.