[gmx-users] charge changes in Free Energy calculations

friendli friendli2000 at gmail.com
Tue Sep 30 04:55:46 CEST 2008

Hi Tsjerk,

I have been thinking about this way, but I do not think have parameters 
for C(-dum)-C to C-C-C, for example, the distance between the 1st and 
3rd carbons.



Tsjerk Wassenaar wrote:
> 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.
> Cheers,
> Tsjerk
> 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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