alchemical transformation

From: Michael A. Wilson (
Date: Thu Aug 17 2006 - 12:04:55 CDT

I have a silly question about alchemical transformation in NAMD. In the examples
in the tutorial, the atoms that are being created and abolished are listed as
separate, charge-neutral groups in the CHARMM topology file. In the case I'm
interested in, the group that contains the atoms to be mutated is quite large,
although we are only mutating a few atoms within the group. The initial and
final groups are charge neutral.

My question is: Does the CHARMM group designation have any significance in
alchemical transformations? If so, can I have atoms that are being created and
destroyed within the same group? If not, does this mean that I will have to
created a second group which duplicates much of the first, and destroy one whole
group while the other whole group is being created?

  Mike Wilson, MS 239-4 (650) 604-5496 day
  NASA Ames Research Center (650) 604-1088 fax
  Moffett Field, CA 94035

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