[gmx-users] radius of gyration

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 11 14:51:15 CEST 2012

On 6/11/12 8:40 AM, delara aghaie wrote:
> Dear Justin.
> Thanks for your explanation.
> ............................................................
> In lyzozyme tutorial the radius of gyration has been plooted against simulation
> time (there 1000 ps).
> When I plot the same graph, the horizontal axis is up to 500 (The number of
> frames for data calculation).
> Although, the gyrate.xvg file has gyration data for these 500 frames, how can I
> tell gnuplot to plot gyration versus simulation time (1000 ps)?

Are you talking about the tutorial or your own data?  If you are talking about 
the tutorial, then the run should have been for 1 ns.  If there are fewer 
frames, then either the .mdp file was changed to specify less time or the 
simulation stopped prematurely.

If you're talking about your own data, I have no way to know what was expected. 
  You can't plot more frames than are present.  I don't use gnuplot so I can't 
offer you any advice as to how you can manipulate the way the data are displayed.



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


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