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

Alexey Romanov Alexey.Romanov at algodign.com
Fri Dec 6 12:59:20 CET 2002

>> >> Hi, GMX users!
>> >> Currently I am working with thermodynamic integration options
>> >> growth) of gromacs (for example - perturbing charges of molecule
>> >> 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
>> that
>> >> it's not correct, because the charges in perturbed molecule have
>> >> effect on other charges of the same molecule, in other words, free
>> >> energy of molecule charging in vacuum must be nonzero. Is it a
>> or
>> >> may be, in Gromacs molecule perturbations are seen only to the
>> >> 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
>> 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.

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