From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Dec 11 2018 - 14:16:10 CST
Hi Randy, indeed if you want to *change* the grid potential during the
lambda transformation I would take Brian's as a complete answer: those
potential terms are ignored by the alchemical code (TI or FEP), and thus
they do not depend on lambda.
Think of gridForces as any other type of restraint: position, symmetry
restraints, Colvars, etc.
Giacomo
On Tue, Dec 11, 2018 at 3:02 PM Brian Radak <brian.radak_at_gmail.com> wrote:
> I would say that there are two kinds of compatibility, which may or may
> not serve your purposes:
>
> 1) can you run dynamics with the added feature?
> 2) does NAMD automate free energy computation with the feature?
>
> I think Giacomo is indicating the former, not the latter. The alchOutFile
> used with ParseFEP only accounts for electrostatic, van der Waal, and
> (optionally) bonded interactions. Any terms not in those classes will be
> ignored from the analysis and the results may or may not be meaningful in
> the way you expect. Even so, you can almost certainly develop your own
> workflow that computes the relevant quantities.
>
> HTH,
> BKR
>
> On Tue, Dec 11, 2018 at 2:46 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hello Randy, the gridForces feature should work in the same simulation
>> with Alchemical FEP, but its forces are not included in the alchemical
>> treatment. This means that the same forces should be applied to atoms
>> being coupled/decoupled, regardless of the value of lambda.
>>
>> I say this based on how each feature is implemented, but you can easily
>> verify it by comparing the potential energy in the MISC column for
>> different alchLambda's.
>>
>> Giacomo
>>
>> On Tue, Dec 11, 2018 at 2:29 PM Randy J. Zauhar <r.zauhar_at_usciences.edu>
>> wrote:
>>
>>> Do usee-defined force field elements, in particular the 'grid-steered’
>>> option, work with alchemical free energy perturbation?
>>>
>>> Thanks!
>>>
>>> Randy
>>>
>>> Randy J. Zauhar, PhD
>>>
>>> Prof. of Biochemistry
>>>
>>> Dept. of Chemistry & Biochemistry
>>> University of the Sciences in Philadelphia
>>> 600 S. 43rd Street
>>> Philadelphia, PA 19104
>>>
>>> Phone: (215)596-8691
>>> FAX: (215)596-8543
>>> E-mail: r.zauhar_at_usciences.edu
>>>
>>>
>>>
>>> “*Yeah the night is gonna fall, and the vultures will surround you / *
>>> *And when you’re lookin’ in the mirror what you see is gon’ astound you*
>>> "
>>>
>>> — *Death Cab for Cutie*, “Monday Morning"
>>>
>>>
>>>
>>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:20:23 CST