Hello together, i refer here to the problem with msd mentioned at the beginning of September (see also below): i calculate msd this time for monomers (not for molecules as before) and i still observe finite size effects for chains if they include fixed bonds ([constrains]), however this effect disappears when i replace fixed bonds by lj+fene bonds. Is it possible that lincs changes (slightly) the velocity field and hence the dynamics?
Regards, Leonid Berk Hess wrote: > Hi, > > g_msd calculates the msd for molecules, not for atoms. > I guess that would explain the result when you half the chain length. > It might also explain the box size effects, since whole chains will > still have a reduction in MSD due to periodiciy with a box of 3 Rg. > > If you run g_msd without -mol you get the MSD per atom. > > Berk > > > From: yel...@uni-mainz.de > > To: gmx-users@gromacs.org > > Date: Thu, 3 Sep 2009 15:22:40 +0200 > > Subject: [gmx-users] msd > > > > Hello together, > > > > i have a problem with msd. i simulate a melt of chain molecules > > consisting of 116 united atoms per chain. then i copy the box n > > times in x,y,z directions, repeat simulations and get a slightly > > different msd curves: > > > > in the time range between 1 ps and 10 ps it flattens out decreasing > > the curvature for larger boxes and at later time (>10ps) follows at > > higher msd just parallel to the curve for smaller box. > > the boxe sizes were tried between 3 to 15 Rg's (gyration radii), so > > if it would be the finite size effect it should already disappear, > but it > > doesnt. > > I also tried with different thermostats (sd, md with nose-hoover), > > different tau_t and also switching off the removal of com (then the > > box starts to fly after awhile) > > > > To check from the other side if it could be the finite size effect i > > reduce the length of the chains from 116 to 58 and the whole msd > > curve shifted up, also in ballistic regime where one can expect no > > influence of chain configuration. interesting that the shift is by > factor > > of ~2 (although is not exactly): perhaps i'm just doing sth wrong! > > msd was calculated for chains using: > > > > g_msd -mol diff_mol.xvg > > > > is anybody aware of such things or has ideas what was done wrong? > > Thanks a lot in advance for any suggestions! > > Regards, > > Leonid > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ------------------------------------------------------------------------ > Express yourself instantly with MSN Messenger! MSN Messenger > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
