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Hi,<br><br>pbc=full is replaced by the mdp option periodic_molecules,<br>which works both with pbc=xyz and pbc=xy.<br><br>Berk<br><br>> Date: Sun, 1 Feb 2009 17:45:13 +0100<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] infinite polymer crystals at gromacs 4.x.x<br>> <br>> Claus Valka wrote:<br>> > Hello,<br>> > <br>> > back in gromacs versions 3.x.x there was the ability to simulate <br>> > (polymer) crystals by enabling the option pbc = full in the mdp file.<br>> > <br>> > That way someone was avoiding the inconsistent shifts message and was <br>> > able to simulate infinite systems.<br>> > <br>> > My question is: now in gromacs versions 4.0 and on, is this feature <br>> > abandoned? <br>> > <br>> > The screw option, which is new, I do not think that replaces the full <br>> > option. The full option is no longer selectable. Is there any other way? <br>> > Or in order to use the files we were using we have to stick with older <br>> > versions?<br>> <br>> It should work by default in 4.0 using pbc=xyz, at least in mdrun. Let <br>> us know if there are problems with other tools.<br>> > <br>> > Yours Sincerely,<br>> > <br>> > Nikos<br>> > <br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <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>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<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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