From: Dave Rogers (wantye_at_gmail.com)
Date: Wed Jul 09 2008 - 21:45:48 CDT
Dear NAMD gurus,
I want to simulate a large protein system and include a
Weeks-Chandler-Anderson (WCA) particle. This would involve adding an
atom to my topology which interacts with other atoms using a shifted
LJ potential out to the minimum, at which point it becomes zero.
Gromacs has a "read pairwise potential from file" option that has
allowed me to do this in the past.
I am thinking I might be able to do the same type of thing in NAMD
by creating a spline lookup table specifically for this
WCA-to-everything interaction, but how do I get NAMD to use this table
instead of the usual one? I have also considered using the tclforces
scripting interface, but this would require me to check all pairwise
distances inside of tcl -- which would by about as efficient as
writing my own MD code (unless I've overlooked something).
What (if any) is the simplest -- i.e. least code modification -- way
you can imagine doing this and your estimated difficulty level (in Lt.
David M. Rogers
Dr. Beck Lab
University of Cincinnati
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