[gmx-users] ED-analysis

[Kavyashree M]

Dear users,

     I have some basic doubts regarding analysis of data:

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.

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?

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?

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.

Thanking you
With Regards
M. Kavyashree
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