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.
-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
--
========================================
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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