Dear all,
I want to perform an alchemical change of state of a molecule in TIP3P,
where I do only change the partial charges of the atomtypes. To control
my results, I perform two MD runs with the different charge sets
respectively.
I'm interested in the Coulomb-14 interactions of the solute (since TIP3P
has none obviously) and would have expected that the potentials of the
end states match those of the classic runs.
For the classic MD, topology A results in -5.74e+02 kJ/mol, while for B
it's -9.04e+02 kJ/mol which seems reasonable.
However, the Coulomb-14 potential of alchemical state A (lambda = 0) is
-5.74e+02 kJ/mol and for state B (lambda = 1) it's -5.69e+02 kJ/mol.
I would have expected that the topology of the alchemical end state B
matches topology B of the MD run, since all parameters should be the
same. The results are the averages given in the log-files.
Are my considerations wrong or could this be a bug in Gromacs?
Thanks,
Andreas
--
M. Sc. Andreas Mecklenfeld
Stipendiat
Technische Universität Braunschweig
Institut für Thermodynamik
Hans-Sommer-Straße 5
38106 Braunschweig
Deutschland / Germany
Tel: +49 (0)531 391-2634
Fax: +49 (0)531 391-7814
http://www.ift-bs.de
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