From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 13 2014 - 15:17:53 CDT
On Tue, May 13, 2014 at 4:09 PM, Michael Bellucci <bellucci_at_mit.edu> wrote:
>
> I see...This is a good point, but then this raises another question.
> Perhaps, I am confused, and maybe you or someone else could provide
> clarity. Say for example, one wishes to compute the free energy of
> solvation of a solute A in a solvent B with thermodynamic integration. The
> mixing Hamiltonian can be written...
>
> H_lambda=(1-lambda)H_1+lambda H_2
>
> where lambda is a scale factor. Let
>
> H_1=K_A+K_B+V_AA+V_BB+V_AB
> H_2=K_A+K_B+V_AA+V_BB
>
> Then the mixing Hamiltonian can be written as...
>
> H_lambda=K_A+K_B+V_AA+V_BB+(1-lambda)V_AB
>
> which is just a standard Hamiltonian with a simple scale factor
> (1-lambda) on the solute-solvent intermolecular interaction. If the
> long-range coulomb electrostatics of solute-solvent interactions cannot be
> scaled since it is a many-bodied term as you suggest, then how exactly does
> the thermodynamic integration code in NAMD handle the solute-solvent scale
> factor? This
>
it is indeed a concern for accuracy. you have to trade off errors. e.g.
from switching to shifted coulomb with a cutoff or applying lambda in a
way that only higher order (and thus shorter range) electrostatic
interactions are created/deleted.
> kind of scaling is similar to what I would like to achieve. Thank you in
> advance!
>
> Mike
>
>
>
> ------------------------------
> *From:* Axel Kohlmeyer [akohlmey_at_gmail.com]
> *Sent:* Tuesday, May 13, 2014 2:56 PM
> *To:* Michael Bellucci
> *Cc:* namd-l_at_ks.uiuc.edu
> *Subject:* Re: namd-l: Scaling solvent-solute intermolecular interactions
>
>
>
>
> On Tue, May 13, 2014 at 2:34 PM, Michael Bellucci <bellucci_at_mit.edu>wrote:
>
>>
>> Dear NAMD users,
>>
>> I would like to know if there is a way to scale down solvent-solute
>> intermolecular interactions while leaving the solute-solute and
>> solvent-solvent intermolecular interactions the same? The closest thing I
>> could find in the NAMD manual was the nonbonded scaling keyword, but this
>> would scale down all intermolecular interactions. I also saw that NAMD is
>> now capable of using tabulated potentials for specific pairwise
>> interactions, but this seems to only be applicable to the VDW
>> intermolecular interaction and not the coulomb interaction. Is there
>> anyway to scale down solvent-solute intermolecular interactions without
>> modifying the source code? Any help or suggestions would be appreciated!
>>
>
> how do you propose to handle long-range electrostatics for this?
> unlike the short range coulomb term, this is not pairwise additive but
> rather a manybody term and thus you cannot partition the interactions in
> the way you want. basically, the amount of scaling would depend on the real
> space cutoff, while normally it can be chosen rather freely to find the
> optimal partitioning between the real space and reciprocal space coulomb
> force calculation.
>
> so you'd be forced to use cutoff-only interactions and then you could
> just set all charges to zero and use tabulation. or use a different MD
> code that has more flexibility (and typically correspondingly less
> performance).
>
> axel.
>
>
>
>
>>
>> Mike
>>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:24 CST