From: Hadi (dinpajooh_at_gmail.com)
Date: Fri Mar 21 2014 - 22:56:50 CDT
Does anybody know how NAMD calculates the excluded Coulombic interactions
in the particle mesh Ewald sum method?
I wanted to compare the NAMD procedure with the one used in the DL_POLY
"For molecular systems, as opposed to systems comprised simply of point
ions, additional modifications are necessary to correct for the excluded
Coulombic interactions. These are intra-molecular bonded interactions and
it is possible to specify these interactions for any given molecular type
on input. In the real-space sum, these are simply omitted. In reciprocal
space however, the effects of individual Gaussian charges cannot easily be
extracted, and the correction is made in real space."
I took a look at the NAMD code to see what method they use for the excluded
Coulombic interactions and it seems to me they do not use the same method
used in DL_POLY.
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