[gmx-users] ED analysis, domain rotation, DynDom

[Tsjerk Wassenaar]

Hi Jo,

First of all, DynDom infers domains, hinges and rotations from two
structures given. It does not provide any information on motion, i.e.
relating to the time-domain. You could extract the structures having
the most extreme projections on a certain mode to further analyse with
DynDom. But mind you that this would not mean there is a straight path
between the two structures. DynDom won't notice if there's a barrier
right in between, preventing going straight from one extreme to the
other. It might require simultaneous motion along another component.

Hope it helps,

Tsjerk

On Thu, Mar 20, 2008 at 5:28 PM, jo hanna <jfhanna at gmail.com> wrote:
> Dear users,
>
> Tsjerk, thanks for your comments, they have been very helpful.
>
> To carry on from that I read this thread:
>
> ##
> [gmx-users] domain Anton Feenstra feenstra at few.vu.nl
> Tue Oct 5 11:43:23 CEST 2004
>
>  smith wrote:
>
> >
>
> > Dear gmx users and David sir,
> >
>
> > I have performed a 10 ns md on a enzyme with two domain structure
> > using gromacs.After the simulation, visualising one of the structures
>
> > picked with largest rmsd showed variation (some movement) of one
> > domain with respect to other.I want to quantitatively measure the
>
> > rotation angle of one domain with respect to other, basiclly analyse
> > it.
>
> >
> > *Is there any tool avilable in gromacs to analyse this conformational
>
> > change.
> > *Can dyndom be used for this purpose by giving the minimized
>
> > structure and md structure as pdb1(conformer1) and pdb2(conformer2)
> > and result obtained.
>
> >
> > *I have not performed Essential dynamics on gmx trajectories, is it
>
> > necessary.
> >
>
> > Can results given by dyndom be interpreted and acceptable for MD
> > simulation.
>
>
> Yes, you can use DynDom for analysis of MD simulations. Most useful way
> is to first do ED analysis, and then DynDom on (several) eigenvector(s),
>
> by first projecting the extremes as a pair of .pdb file (use g_anaeig),
> and feeding the pair of .pdf files to DynDom.
>
>
>
> --
> Groetjes,
>
> Anton
> ###
>
> I am wanting to use Dyndom in the way described above but am not quite sure
> about the reference to the pair of pdb files. Would a way to do this be to
> say project the first and second eigenvector and then use Dyndom to compare
> the starting structure with the first eigenvector extreme pdb and then do
> the same for the second? Would this show the evolution of the motions
> throughout the simulation?
>
>
> Thanks and please accept my apologies if the answer to this question is
> obvious,
> Jo
>
>
>
>
> On Sat, Mar 8, 2008 at 10:49 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> > Hi Jo,
> >
> > First of all, you should note the difference between essential
> > dynamics analysis and sampling. Also note there's nothing essential
> > about it. But the first is done using g_covar/g_anaeig and the latter,
> > which concerns enhanced sampling along specific modes, is done using
> > make_edi/mdrun. So in your case, you want the first.
> >
> > As to the question regarding the group for fitting, what you'll do if
> > you fit to one domain and calculate the covariance matrix for the
> > whole thing is, sort of, amplifying the inter-domain motion, while
> > suppressing the influence of the local motions. As the displacements
> > of the other (non-fitted) domain will be much larger, the covariances
> > involving these motions will also be the larger ones. Maybe this is
> > just what you want. It is explained in a (little) bit more detail in
> > our Proteins paper from this month.
> >
> > Finally, whether to use deviations from a reference are from an
> > average. I'd say the results are better defined if you use deviations
> > from the average, as you'll be talking about central moment principal
> > components. Non-central principal component analysis requires a lot
> > more thought and explanation.
> >
> > Try to read some statistics literature on principal component analysis
> > to get more feel for the method (and at any point realize that wer'e
> > so lucky to be able to give physical meaning to the components we get
> > ;)).
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> >
> >
> >
> > On Fri, Mar 7, 2008 at 11:50 PM, jo hanna <jfhanna at gmail.com> wrote:
> > > Hi
> > >
> > > I have a done number of MD simulations of a two domain protein with
> > > different ligands and also in the apo state. Comparing these simulations
> I
> > > see varying degrees of domain rotation of the one domain relative to the
> > > other which I want to quantitatively measure and I was thinking of using
> > > DynDom to do this; I have already assessed a number of structures taken
> from
> > > different points throughout the simulations but want a to assess the
> motion
> > > throughout the simulations.
> > >  >From the user lists I read that I should do ED analysis first. Is this
> > > using g_covar and then g_anaeig or using make_edi and then doing ED in
> mdrun
> > > and then assessing these results?
> > > Also as the motion appears to be the C-terminal domain relative to the
> > > N-terminal domain when using g_covar should I fit over the N-terminal
> domain
> > > backbone but do the analysis over the whole backbone, or just fit over
> the
> > > whole backbone? Also in g_covar is it better for this type of problem to
> use
> > > the -ref option and assess the deviation from the conformation in the
> > > structure file instead of from the average?
> > > I would appreciate some guidance as although I've read some papers on
> this
> > > subject I am a bit confused as to what is the best way to progress.
> > >
> > > Many thanks,
> > >
> > > Jo.
> > > _______________________________________________
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> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
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>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623