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

[David van der Spoel]

On Fri, 2002-12-06 at 12:59, Alexey Romanov wrote:
> >> >> 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?
> >> I think, propane is large enough to have intramolecular charge and
> Van
> >> der Waals interaction in OPLS.
> >yes, but only H-H and H-C, don't know whether H's have VDW in OPLS,
> >charge they do.
> 
> OPLS nonpolar H have charges and VdW parameters.
> I just tested butane. Always zero free energy!
> In my case every atom in butane have charge and VdW parameters.
> But energy is zero in perturbing either charges or VdWs to zero.
> Strange thing.
> Regards,



did you set the appropriate options in the mdp file?



> Alex.
> 
> 
> 
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-- 
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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