[gmx-users] Free energy for charged molecules

[Ignacio Fernández Galván]

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.

Thanks


		
___________________________________________________________ 
To help you stay safe and secure online, we've developed the all new Yahoo! Security Centre. http://uk.security.yahoo.com