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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>This issue is caused by the use of domain decomposition instead<br></div>particle decomposition.<br><br>However, this does not have much to do with the "nojump" behavior<br>you are talking about.<br>The pbcatom is only used for determining the COM of one group.<br>The distance between COM's was always done with full pbc,<br>which means that the vector between the two closest images is used.<br><br>Note that the choice of pbcatom only has an effect for groups with<br>and x, y or z size that is more than half the box length.<br>(and it does not at all affect how the distance between groups<br>is determined)<br><br>Berk<br><br><br><hr id="stopSpelling">> Date: Thu, 30 Oct 2008 13:16:56 -0400<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] pull_pbcatom1 and pull code in gromacs 4<br>> <br>> Hello,<br>> <br>> The pull-code .mdp option pull_pbcatom1 is defined in the online manual as:<br>> <br>> "The reference atom for the treatment of periodic boundary conditions <br>> For determining the COM, all atoms are put at their periodic image which <br>> is closest to pull_pbcatom1. A value of 0 means that the middle atom <br>> (number wise) is used."<br>> <br>> I suppose that this is necessary since mdrun now writes broken <br>> molecules. However, this is suboptimal for replica exchange umbrella <br>> sampling (pull = umbrella, pull_geometry = distance) in which one does <br>> not necessarily want to utilize different periodic images of pull_group0 <br>> and pull_group1.<br>> <br>> a) Perhaps I don't understand. Is it possible that although a particular <br>> image of each pulled group is chosen, the pulling is actually still done <br>> along the vector between the closest two images?<br>> <br>> b) If not, is there a simple code modification to utilize a pbc=nojump <br>> type definition here during dynamics?<br>> <br>> Thanks,<br>> Chris.<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.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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