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Hi,<br><br>If something is periodic or cyclic only depends on the coordinates,<br>in the topology there is no difference.<br>That is the reason for the periodic_molecules mdp option.<br><br>You will have to manually add the bond, angles, dihedrals and pairs<br>for the periodic (or cyclic) bond to the topology.<br><br>Berk<br><br>> Date: Tue, 1 Sep 2009 10:37:11 +0300<br>> From: neamtuandrei@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] periodic moleules<br>> <br>> Hi,<br>> <br>> I am trying to build a hydrogel polymeric system and I want to make<br>> use of the option periodic_molecules.<br>> In this regard I am a little bit confused..... are there any other<br>> keywords except the option 'peridic molecules' that I have to set to<br>> define a periodic polymer chain e.g. in the molecular topology file?<br>> Because in the case I define a bond between the last atom of the<br>> chain and the first one, how does the grompp and mdrun know that the<br>> molecule is periodic and not cyclic?<br>> <br>> I also suppose that the angle and dihedrals that cross the periodic<br>> border should also be defined.<br>> <br>> Is there a place where I can find how to define periodic molecules in Gromacs?<br>> <br>> Thanks a lot for any suggestions,<br>> <br>> Andrei<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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