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
