[gmx-users] How to the define the A and B states for the calculation of free energy

xu zhijun simulationxu at yahoo.com
Sun Jan 15 01:55:41 CET 2012

Thanks Justin.

You mean I put the na+ and Ca+ in the same "moleculetype"?

But I just worry about whether it is feasible to put the two ions in the same moleculetypes even if they have no any connects between them (bond, angle).

Thanks again.

--- On Sat, 1/14/12, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] How to the define the A and B states for the calculation of free energy
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Saturday, January 14, 2012, 7:33 PM

xu zhijun wrote:
> Hi gromacs-users,
> I have carefully checked the manual about the define the A and B states for the calcualtion of free energy. And I also known that "couple-moltype“ and "couple-lambda0" and "couple-lambda1".
> However I have two types of molecules for decoupling in the simulaiton. It seems that Gromacs can not deal with more than one tpes of moleucle with the "couple-moltype".
> For example I want to decouple the Na+ and Ca+. Is the the other way to define the decoupling molecules? It seems that I can directly define the B state in the top files for these two ions, repectively. If it is reasonable, does the other molecules without the descrption of the B state keep fixed? (I mean these molecuse will not involve the decoupling process in the simulation.)

If there is not a defined B-state, then parameters from the A-state are applied, hence no transformation.  Another approach is to hack the topology such that the ions you want to decouple are all in the same [moleculetype].


-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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