[gmx-users] Combined essential dynamics analysis

barrett barrett at biop.ox.ac.uk
Wed Jul 16 13:46:01 CEST 2003

I have tried to do something very similar, and found similar results.

Perhaps you have some idea of what differences you are expecting: have a
look at the output of DISCO (in vmd or something). This will show you
whether that difference is indeed occurring. E.g. I expected a loop to
be loose in one and tethered in the other. It was in fact tethered in

I concluded that the problem was as follows (I could be wrong: Bert etc
please feel free to correct):

The change I made, removal of a phosphate makes a big difference in
reality because it happened to be the one atom that really was holding
the loop in place. Indeed in MD you do see the loop move when phosphate
is removed. The program DIST however makes up lots of constraints and I
think that in my case it made up some constraints that in fact get
broken in nature at 300K. Therefore DIST disallowed physically
realizable reconfigurations.

My only suggestion is that you could go into the output of DIST and
manually remove suspect looking constraints. However this is not very
practical unless you know what you are looking for. Sorry.

I have concluded that CONCOORD sometimes struggles to choose the right
constraints in a molecule that in nature is able to undergo a

I would be very interested if you find a fix to this...

Paul Barrett

Dr Paul Barrett
Laboratory of Molecular Biophysics
Department of Biochemistry
University of Oxford

Tel 01865 275191
Fax 01865 275182

barrett at biop.ox.ac.uk
hellopaul1 at hotmail.com


-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
On Behalf Of Ruben Martinez Buey
Sent: 16 July 2003 21:04
To: gmx-users at gromacs.org
Subject: [gmx-users] Combined essential dynamics analysis

Hi all,
I´m trying to compare two similar systems (one with a ligand and the
without it). I´ve used CONCOORD for both systems. I´ve concatenated the
individual trajectories and run g_covar over the concatenated
trajectory. Only
the first 5-7 resulting combined eigenvectors are significant.
When I project the individual trajectories over these combined
eigenvectors, I
get the next results:

Average projection (mean):
eigenvec 1: -0.365220            0.457450
eigenvec 2:   0.137630          -0.169460
eigenvec 3:   0.137790          -0.319940
eigenvec 4:   0.068647          -0.078291
eigenvec 5:   0.087228            0.040858

Mean square fluctations (stddev):
eigenvec 1:   6.7204                 6.7390
eigenvec 2:   3.9814                 4.2909
eigenvec 3:   3.6093                 3.6686
eigenvec 4:   2.3390                 2.2201
eigenvec 5:   1.8614                 1.8681

(Where the first column is the protein with the ligand, and the second
is the protein without ligand)
But the extreme projections over each eigenvector (generated by
g_anaeig) are
exactly the same in both cases. So, what would be the conclusion? There
are no
significant differences in the essential dynamics beetwen both systems?
But the
differences in the average projections are large enough to be
aren´t they? And the

Thanks in advance for your kind attention,
with best wishes,

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