[gmx-users] rmsd fluctuation of the dihedrals

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 9 20:40:37 CET 2008

Prasad Gajula wrote:
> Dear Gromacs users,
> can some one give me a hint to calculate the " rmsd fluctuation of the
> dihedrals"  to see the angle dynamcis.
compute the angles as a function of time (g_angle), then use xmgrace to 
compute the fluctuations.note that dihedrals are periodic, so averages 
and fluctuations may not make much sense. You are better of with a 
distribution (g_analyze on the results of g_angle).
> thanks in advance
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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