[gmx-users] secondary structure movments

라지브간디 rajiv at kaist.ac.kr
Fri Jan 18 08:46:36 CET 2013


Dear Justin,

For example, In hemoglobin (A-H helix), the particular E and F helix gets moved during the MD simulation, I would like to calculate this helix movements/rotation angle? Thanks.

 Dear all, 
> I have been trying to calculate and plot the secondary structure of helix movements during the simulation on time through g_helix, g_helix orient, g_principle and g_mindist but none of them shown the helix movements. 
> Is there any other tool can elaborate the helix movements ? Plz suggestion are appreciated. 

You'll have to define what you mean by "helix movements." Everything moves in a 
simulation, but what is it that you're trying to quantify? If it's secondary 
structure itself, use do_dssp. If you're after something else, you will have to 
be more specific. 


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