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Hi,<br><br>I would think any system with a membrane in it is too large to gain much with REMD<br>(unless you are interested in the temperature dependence).<br><br>You can use essential dynamics sampling or flooding, see make_edi.<br><br>Berk<br><br>> Date: Fri, 20 Nov 2009 10:00:11 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Pushing MD further<br>> <br>> <br>> <br>> Thielges, Sabine wrote:<br>> > Hi,<br>> > <br>> > I am currently running some GPRC MD with membrane. After a lot of trial<br>> > I now have a nice 25 ns run with an agonist. But the final structure is<br>> > too close the starting and I know it is far from what the biology<br>> > describes. <br>> > I would like to know if there is options that I can add to my md.mdp<br>> > file to make the MD "explores some other area". <br>> > <br>> <br>> There is no magic .mdp option to make sampling better, and you can not <br>> necessarily ever trust the results of just one single simulation. There are <br>> several options to enhance sampling:<br>> <br>> 1. Simulated annealing<br>> 2. Replica-exchange MD<br>> 3. Additional simulations with different starting velocities<br>> <br>> With #2, bilayers can be quite problematic. A recent paper from Max Berkowitz's <br>> group in JPCB has a nice protocol for REMD with a membrane.<br>> <br>> -Justin<br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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