[gmx-users] ED-analysis

[Kavyashree M]

Dear Sir,

   Thank you sir for the clarification. But if there is only one
polymer (protein) with water in the system then also is it
necessary because in one of the mails -
http://lists.gromacs.org/pipermail/gmx-users/2010-October/055320.html
there was a discussion regarding this topic. So I wanted to
ensure regarding that

It is absolutely necessary that the molecules be whole, and in the
> case of multimers, correctly assembled.
>

But if there is only one polymer (protein) with water in the system
then also is it necessary to use nojump or mol in trjconv?because
in one of the mails -

http://lists.gromacs.org/pipermail/gmx-users/2010-October/055320.html

there was a discussion regarding this topic. So I wanted to
ensure regarding that aspect. Molecule after simulation
crosses the box boundary in the simulation I have done, So
if I processed analyzing with the native .xtc file there will be
a problem? But in this case its a single intact protein molecule
in water.


> Worse, the first eigenvector can be dispersed over the second and
> third in another (equivalent) system. But this is what the RMSIP is
> for. It is a measure to indicate how much one set of eigenvectors
> corresponds to another, regardless of the order.
>


> Yes, it is absolutely necessary that the conformational space is
> defined in the same way for the different systems. Let's say you have
> a set of configurations X, for which you determine the covariance
> matrix and the eigenvectors/-values:
>
> S = (1/N)XX' = PDP'
>
> Now take the same system, but rotated:
>
> T = (1/N)RXX'R' = RPDP'R'
>
> So the eigenvectors for the rotated configurations are rotated too.
>

Ok.


> > 4. Kindly provide a clear protocol for the essential dynamics
> >     analysis of 4 proteins with different sequence length and
> >     sequence similarity. but the native structures superpose
> >     very well 3 dimensionally.
>
> This is up to you... Sorry.
>

I will find a way. Thank you sir..

Thanking you
With Regards
M. Kavyashree
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