[gmx-users] concoord problem

Bert de Groot bgroot at gwdg.de
Tue Jul 27 18:34:49 CEST 2004

Hi John,

In general, please don't clutter the gmx list with (off-topic) concoord questions. Instead,
send them to me. If I don't answer soon enough, you can always decide to try the gmx
list afterwards ;-)

But in this case your question is mainly a g_covar/g_anaeig one. If you get distorted structures
with the -extreme option that simply means the there were large fluctuations in your trajectory
which can not be described by (linear) eigenvectors such that the structure still looks like
a protein. This is not necessarily a problem, only a bit awkward for visualisation.
This usually happens with trajectories that contain e.g. domain rotations of more than approx.
30 degrees or so. To get a more appealing visualisation, you can decide to focus only on the
"central part", i.e. smaller amplitude rotations, use the "-damp" option of concoord, or use more
eigenvectors to correctly capture the non-linear motions of  your system.

Concerning your question about mutations in concoord:
concoord generates based on a known structure, or "around" a known structure in
configurational space. Concoord won't, like e.g. MD, show a structural transition, or
drift due to e.g. a mutation. What can be seen usually is a shift if the average structure
due to a mutation (so between an WT and mutant ensemble). In a PCA analysis such
a shift can be recognised when the two trajectories are combined in one PCA and
differences in behaviour (averages, fluctuations) occur between the different trajectory
parts when projected onto single eigenvectors. These shifts along eigenvectors can
be small, but they may be significant, as concoord hardly suffers from a sampling problem
(when at least a few hundred structures are generated).


Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de

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