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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> Date: Sun, 3 Feb 2008 10:46:28 +0100<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] exchanged pairs in the log file of a remd simulation<br>> <br>> OZGE ENGIN wrote:<br>> > Hi all,<br>> > <br>> > I am performing replica exchange MD simulations. Here, I attach the part of a log file which gives info about the exchanges made at step 46000 and 47000. It is just a test run. As you can see, on the line 2, it is indicated that the exchange is made between the rep 1 and rep 2 or between the repl2 and repl3. The case is the same for other time steps.<br>> > There are no other types of pairs. <br>> > <br>> > Why?<br>> > <br>> Other exchanges are not attempted, although this is not entirely <br>> correct. However since the probability for exchanges is ver small when <br>> the energy overlap is small this is not a serious approximation. In your <br>> case it seem like you have quite high probabilities however, indicating <br>> that your temperature spacing is quite small. In that case exchanges 1-3 <br>> could be possible, but these are not attempted in gromacs.<br><br>This is not a matter of correctness.<br>The scheme in Gromacs in completely correct.<br>The pairs that are chosen for attempt are not chosen based on their energy or exchange probability,<br>so there is no bias.<br>It is only a matter of efficiency.<br>It would be slightly more efficient to try to exchange all pairs.<br>But then you do get into matters of correctness.<br>When I first try to exchange replicas 1 and 2, the result depends on the energies of replicas 1 and 2,<br>an exchange of 2 and 3 will therefore not only depend on the energies of 2 and 3, but of 1, 2 and 3.<br>Maybe this is not incorrect, but to avoid this issue and to simplify the practicalities of exchanging the states,<br>I decided to alternate the odd and even pair attempts.<br><br>Berk.<br><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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