[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 02:19:45 CET 2012

Thanks a lot Justin.

Have a good night.

PS: the gromacs tutorials in your home page are really pretty good. 

--- 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, 8:04 PM

xu zhijun wrote:
> 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).

The chemical definition of a molecule and the Gromacs definition of a moleculetype are completely unrelated.  In theory, you could put all of the molecules in your system in a single moleculetype.  It's simply a topology construct for organization.


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

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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