[gmx-users] Movements of secondary structure

Justin Lemkul jalemkul at vt.edu
Fri Jan 18 02:57:11 CET 2013

Please use an appropriate subject line and delete irrelevant parts of the digest.

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.


> 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


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list