Thank you for all your replies. Actually, I have already applied trjconv -pbc. So I'm sure that my analysis is on a whole protein, centered in my box. I'm using gromacs 4.0.3 So I think that you were right by saying that my dimer is not stable while my monomers are. But now, I have to fgure out why.
Thanks again, Carla On Wed, Jun 30, 2010 at 1:54 PM, Tsjerk Wassenaar <[email protected]> wrote: > Hi, > > > Not necessary! > > If the dimer separates across the boundaries you have > > a problem of fitting the two together while they are separated. > > This is only if you use the dimer. The monomers would be fine. > > That was the case before gromacs 4. But the current versions don't > keep molecules whole. This means that a PBC effect will show up in at > least one monomer, if there is splitting over the boundaries. It also > means that the jumps due to this are much smaller, and may not be as > easily identified as before. That's a general word of caution, > unrelated to the issue mentioned here. > Concluding, if the version is <4, the increase in RMSD may either be > due to splitting or due to relative motion of the domains, but the > evolution of the RMSD (sudden or gradual) will tell which is the case. > Otherwise, the increase will be due to relative motion of the domains. > > Cheers, > > Tsjerk > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolecular Research and Biotechnology > University of Groningen > The Netherlands > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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