[gmx-users] Re: Trying to replicate Aqvist's results (solvation free energy).
chakrabarty.suman at gmail.com
Mon Aug 12 07:17:17 CEST 2013
(I am re-posting this since my earlier messages seem to be rejected by the
mailing list. Please ignore if you are receiving this multiple times.)
One possible origin of the difference might be the usage of either a
counter-ion or a background negative charge to neutralize your system
when you are using PME within PBC. In spherical boundary condition,
there is no such requirement of a neutral system and you can calculate
the absolute free energy of creating a charge in the system.
So the difference might be accounted by the interaction of the
positive charge in your system with the background negative charge. I
don't think Aqvist's results can be reproduced using PME/PBC. May be
you can check with the reaction-field electrostatics, but again Aqvist
uses a special surface constraint for the water sphere (SCAAS model by
Warshel), which is missing in Gromacs reaction-field treatment
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