Re: User force field with FEP?

From: Randy J. Zauhar (r.zauhar_at_usciences.edu)
Date: Tue Dec 11 2018 - 14:01:04 CST

Thanks Giacomo. So only ‘force field’ potentials are usable in FEP, anything else has to be done by TI?

It would be nice if potentials could be coupled to a ‘lambda schedule’ for use in FEP.

Randy




On 11Dec, 2018, at 2:44 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto: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<mailto: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<mailto: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

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<mailto: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"



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