[gmx-users] g_covar on multiple simulations

Bert de Groot bgroot at gwdg.de
Fri Sep 19 11:57:01 CEST 2003

Anton Feenstra wrote:
> Hi,
> Does anyone have experience in g_covar (essential dynamics) on multiple,
> combined, trajectories? My experience for single (or a few comined)
> simulations, is that only a few (<10, sometimes <5) eigenvectors capture
> about 60% of MSF, but in the case I'm studying now (Cyt.P450), 12 are
> needed for 60%, and 30 for 80%...!
> Is this unusual, 

kind of, mostly it's more concentrated

> or have other people seen similar things?

no. I've done plenty combined analyses and always have had the majority
of the MSF concentrated in a low-dimensional subspace. I can see two reasons
for your observation:

1) a fitting/alignment inconsistency. Are you sure that the (sub)set of
atoms you extract from each trajectory match exactly to each other and
to the reference (-s in g_covar) structure? Taking a few snapshots and
superimposing them with g_confrms usually helped me to identify such problems.
Large jumps from one trajectory piece to the next in the projections 
of the combined trajectory onto the eigenvectors might also be a sign.
2) your protein is kind of floppy and different modes are sampled in
different trajectories. Is the MSF more concentrated in PCA's from single
trajectories than in the combined trajectory?



Dr. Bert de Groot

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

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de

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