Re: alchemical transformation

From: Jerome Henin (jhenin_at_vitae.cmm.upenn.edu)
Date: Thu Aug 17 2006 - 14:44:27 CDT

Dear Mike,

Unless I am mistaken, CHARMM charge groups are simply ignored by NAMD, so
there cannot be any interference with alchemical transformations.

Best,
Jerome

On Thursday 17 August 2006 13:04, Michael A. Wilson wrote:
> 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?
>
> Thanks,
> Mike
>
> ___________________________________________________________________________
>__ 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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