[gmx-users] Movements of secondary structure

[Justin Lemkul]

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On 1/17/13 8:42 PM, 라지브간디 wrote:
> 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.
>

RMSD (g_rms and/or g_rmsf -od), intramolecular distances (g_dist), helical 
rotation (g_helix) should all provide useful information.  Please consult 
Chapter 8 of the manual to understand the quantities that Gromacs can calculate 
and the methods for doing so.

-Justin

> 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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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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