[gmx-users] Free energy for charged molecules

Ignacio Fernández Galván jellby at yahoo.com
Wed Sep 20 09:25:17 CEST 2006

Hi all,

Is there some precaution or additional term I should take into account
when calculating the free energy of solvation for a charged molecule?

I plan to make the molecule "disappear" whith lambda moving from 0 to 1
and then perform a thermodynamical integration, this seems to work
reasonably well for neutral molecules. Is there any "gotcha" with
charged molecules? Of course, I'm using PME, pbc=xyz and a large enough
simulation box.


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