[gmx-users] charge changes in free energy calculations
friendli2000 at gmail.com
Fri Oct 3 08:58:45 CEST 2008
Thanks for clarification.
Yes, you are right. I am morphing only parts of the sidechain.
David Mobley wrote:
> 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
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