[gmx-users] ED-analysis

[Tsjerk Wassenaar]

Hi Kavya,

> 1.  Can the .xtc file from MD be used directly for analysis
>      without applying -pbc nojump or mol option? [I had
>      asked the same question before but was not clear
>      with the answer.

It is absolutely necessary that the molecules be whole, and in the
case of multimers, correctly assembled.
>
> 2.  While calculating the RMSIP (root mean square inner
>     product) suppose the 10 eigen vectors in one simulation
>     is not in the same order as in the second simulation ie.,
>     the first ranked eigen vector in one simulation is equivalent
>     to second ranked eigen vector in another simulation
>     being compared - How can this ambiguity be taken care of?

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.

> 3. Before comparing two ED simulations is it required to align
>     all the structures to only one initial structure? As the orientation
>     of the two initial structures may differ?

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.

> 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.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands