[gmx-users] FW: about atom perturbation in TI

Alexey Romanov Alexey.Romanov at algodign.com
Fri Dec 6 09:05:37 CET 2002

-----Original Message-----
From: Alexey Romanov [mailto:Alexey.Romanov at algodign.com]
Sent: Wednesday, December 04, 2002 1:12 PM
To: 'gmx-users at gromacs.org'
Subject: about atom perturbation in TI

Hi, GMX users!
Currently I am working with thermodynamic integration options (slow
growth) of gromacs (for example - perturbing charges of molecule to
nothing in water solvent).
All works fine, but when I try to do this for molecule in vacuum
(without solvation), I always get zero free energy change. I think, that
it's not correct, because the charges in perturbed molecule have an
effect on other charges of the same molecule, in other words, free
energy of molecule charging in vacuum must be nonzero. Is it a bug, or
may be, in Gromacs molecule perturbations are seen only to the other
Alex Romanov,
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