[gmx-users] ED analysis, domain rotation, DynDom
tsjerkw at gmail.com
Thu Mar 20 20:27:04 CET 2008
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,
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.
> 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
> 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
> > > 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
> > > different points throughout the simulations but want a to assess the
> > > 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
> > > 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
> > > backbone but do the analysis over the whole backbone, or just fit over
> > > whole backbone? Also in g_covar is it better for this type of problem to
> > > 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
> > > 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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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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