[gmx-users] charge changes in free energy calculations

David Mobley dmobley at gmail.com
Thu Oct 2 21:14:39 CEST 2008


As long as you end up with the same charge in the initial and final
states,  you should be OK. It's only if your total transformation
involves a change of net charge that you need to worry. So you should
be fine if you turn off the charges on D, change the LJ interactions,
and turn back on the charges on E.

If I were you, I probably would not turn off the charges entirely --
after all, D and E share many atoms. I would only turn off charges on
the atoms that you are going to modify.


On Fri, Sep 26, 2008 at 2:14 AM, friendli <friendli2000 at gmail.com> wrote:
> Dear all,
> I have a mutation free energy calculation from D(asp) to E(glu). The charge
> is not changed for the overall mutation. However, following Dr. David
> Molbey's suggesion, electrostatic and VDW interaction should be modified
> separately, so in the first step we need to turn off the charge from D(-1)
> to D(0).
> I learn from the mailing list that it is problematic to do FE calculations
> with different charges for initial and final states.
> So is that safe to turn off the charge for D and turn on the same charge for
> E in this case?
> If not, it that OK to perform mutation FE calculation in one step?
> or there is no safe way to handle this kind mutations, i.e. mutating charge
> groups, currently without special correction?
> thank a lot
> Qiang
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