From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Sat Jul 23 2011 - 02:44:36 CDT
Hi Esmael,
If the process is charging the particles, then you want "alchDecouple
off". With alchDecouple, the process would be turning on electrostatic
coupling between the pair of particles and the solvent. If the
Just a reminder: you don't need a "dual topology" setup for this
transformation: just set both alchElecLambdaStart and alchVdwLambdaEnd
to 0.5 and look at the lambda interval between 0.5 and 1 (assuming the
FEP flags for them are set to 1, so they behave as "appearing"
particles, not "disappearing").
Cheers,
Jerome
On 23 July 2011 02:10, esmael <haddadian_at_uchicago.edu> wrote:
> Hi,
> I am trying to calculate the free energy of charging two spherical particles
> in water fixed at a given distance using the FEP within NAMD. These two
> particles are not bonded; should I set the "alchDecouple" to on or off? I
> would like that these two particles "see" each other and interact during the
> course of FEP calculations (and the interaction energy be included in the
> total free energy).
> Thanks a lot,
> Esmael
>
>
>
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