[gmx-users] FW: about atom perturbation in TI
David van der Spoel
spoel at xray.bmc.uu.se
Fri Dec 6 13:05:04 CET 2002
On Fri, 2002-12-06 at 12:00, 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,
> >> 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,
> >> may be, in Gromacs molecule perturbations are seen only to the other
> >> molecules?
> >> Regards
> >Is there normal intramolecular interaction energy in the molecule?
> >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.
> >Groeten, David.
> Regards, Alex
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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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