[gmx-users] Dimer g_rms

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jun 30 13:54:35 CEST 2010


> 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.



Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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