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Hi,<br><br>g_msd calculates the msd for molecules, not for atoms.<br>I guess that would explain the result when you half the chain length.<br>It might also explain the box size effects, since whole chains will<br>still have a reduction in MSD due to periodiciy with a box of 3 Rg.<br><br>If you run g_msd without -mol you get the MSD per atom.<br><br>Berk<br><br>> From: yelash@uni-mainz.de<br>> To: gmx-users@gromacs.org<br>> Date: Thu, 3 Sep 2009 15:22:40 +0200<br>> Subject: [gmx-users] msd<br>> <br>> Hello together,<br>> <br>> i have a problem with msd. i simulate a melt of chain molecules <br>> consisting of 116 united atoms per chain. then i copy the box n <br>> times in x,y,z directions, repeat simulations and get a slightly <br>> different msd curves:<br>> <br>> in the time range between 1 ps and 10 ps it flattens out decreasing <br>> the curvature for larger boxes and at later time (>10ps) follows at <br>> higher msd just parallel to the curve for smaller box. <br>> the boxe sizes were tried between 3 to 15 Rg's (gyration radii), so <br>> if it would be the finite size effect it should already disappear, but it <br>> doesnt.<br>> I also tried with different thermostats (sd, md with nose-hoover), <br>> different tau_t and also switching off the removal of com (then the <br>> box starts to fly after awhile) <br>> <br>> To check from the other side if it could be the finite size effect i <br>> reduce the length of the chains from 116 to 58 and the whole msd <br>> curve shifted up, also in ballistic regime where one can expect no <br>> influence of chain configuration. interesting that the shift is by factor <br>> of ~2 (although is not exactly): perhaps i'm just doing sth wrong!<br>> msd was calculated for chains using: <br>> <br>> g_msd -mol diff_mol.xvg<br>> <br>> is anybody aware of such things or has ideas what was done wrong?<br>> Thanks a lot in advance for any suggestions!<br>> Regards,<br>> Leonid<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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