<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Thanks Justin.<br>
<br>
You mean I put the na+ and Ca+ in the same "moleculetype"？<br>
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).<br><br>Thanks again.<br><br><br>--- On <b>Sat, 1/14/12, Justin A. Lemkul <i><jalemkul@vt.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Justin A. Lemkul <jalemkul@vt.edu><br>Subject: Re: [gmx-users] How to the define the A and B states for the calculation of free energy<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Saturday, January 14, 2012, 7:33 PM<br><br><div class="plainMail"><br><br>xu zhijun wrote:<br>> Hi gromacs-users,<br>> <br>> 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".<br>> 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".<br>> 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.)<br>> <br><br>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].<br><br>-Justin<br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of
Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org"
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