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

[xu zhijun]

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

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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