[gmx-users] charge changes in Free Energy calculations

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Sep 29 11:19:37 CEST 2008

Hi Qiang,

Couldn't you do it by shortening the chain, turning on/off one of the
CH2 groups? You only have to mind perturbing the bonding and such in
the right way then.



On Sat, Sep 27, 2008 at 6:32 PM, 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
> Mobley's suggetion, 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?
> thanks a lot
> Qiang
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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