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 <[email protected]> wrote: From: Justin A. Lemkul <[email protected]> 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" <[email protected]> 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 -- ======================================== 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 ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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