[gmx-users] domain

[smith]

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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.  
  
  
Any suggestion and comments on this is welcome.thanking in advance  
  
smith.  
cheers