From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Jul 25 2011 - 15:19:14 CDT
On 25 July 2011 20:10, esmael <haddadian_at_uchicago.edu> wrote:
> Hi Jerome,
> Thanks a lot for the reply. I think your response has somehow been cut in the second paragraph.
Sorry, that was just a bit of misplaced cut-and-paste, courtesy of my
> I am only interested in Electrostatic interactions and therefore I am was using
> ElecLambdaStart=0.0 and alchVdwLambdaEnd=0.0; would this be OK?
I didn't suggest that because I was not sure if it would trigger a
divide-by-zero condition somewhere, but if you have tried it and it
doesn't crash, then you're fine.
> On Jul 23, 2011, at 2:44 AM, Jérôme Hénin wrote:
>> 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").
>> On 23 July 2011 02:10, esmael <haddadian_at_uchicago.edu> wrote:
>>> 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,
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