Re: User force field with FEP?

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Dec 11 2018 - 14:02:12 CST

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
>

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