[gmx-users] g_covar on multiple simulations

[Marco Ceruso]

Hi-
The number of eigenvectors to describe the essential motions of the protein
will depend on its rigidity, the more rigid the more eigenvectors.
I have had similar cases i.e. 30 egv for 80% just from one traj (314 Ca)
Marco

-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Anton Feenstra
Sent: Friday, September 19, 2003 6:27 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] g_covar on multiple simulations


Bert de Groot wrote:
> 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.

Seems unlikely, I have a WT and 3 point mutants and select C-alpha. That
is 455 atoms for all simulations, also all starting points in the 2d
projection are very close as they should since the structures are nearly
identical for the point mutants.

> 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?

Working on that right now... Running multipe g_covar's and will calculate
matrix of subspace overlaps for 43 simulations... ;-)


--
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
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|             | Costello)                                             |
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