Dear users,<br><br> I have some basic doubts regarding analysis of data:<br><br>1. Can the .xtc file from MD be used directly for analysis<br> without applying -pbc nojump or mol option? [I had <br> asked the same question before but was not clear <br>
with the answer.<br><br>2. While calculating the RMSIP (root mean square inner<br> product) suppose the 10 eigen vectors in one simulation<br> is not in the same order as in the second simulation ie.,<br> the first ranked eigen vector in one simulation is equivalent <br>
to second ranked eigen vector in another simulation<br> being compared - How can this ambiguity be taken care of?<br><br>3. Before comparing two ED simulations is it required to align<br> all the structures to only one initial structure? As the orientation <br>
of the two initial structures may differ? <br><br>4. Kindly provide a clear protocol for the essential dynamics <br> analysis of 4 proteins with different sequence length and <br> sequence similarity. but the native structures superpose <br>
very well 3 dimensionally.<br><br>Thanking you<br>With Regards<br>M. Kavyashree<br><br><br><br>