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

Alexey Romanov Alexey.Romanov at algodign.com
Fri Dec 6 12:00:12 CET 2002

>> 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.

>Groeten, David.

Regards, Alex

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