[gmx-users] Dimer g_rms

Carla Jamous carlajamous at gmail.com
Wed Jun 30 14:07:51 CEST 2010

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,

On Wed, Jun 30, 2010 at 1:54 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> 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
> --
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