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

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 6 10:09:55 CET 2002

On Fri, 2002-12-06 at 09:05, Alexey Romanov wrote:
> -----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
> molecules?
> Regards
Is there normal intramolecular interaction energy in the molecule? Could
it be due to exclusions?

> Alex Romanov,
> Moscow.
Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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