Re: how to get the plot of selected bond over time?

From: Alessandro Pedretti (
Date: Fri Dec 05 2003 - 07:19:45 CST

VEGA OpenGL allows to analyze the DCD output generated by NAMD (e.g.
distance, angle, torsion, angle between two planes, dipole, surface, lipole,
etc) with a point & click interface. If your system is very complex, you can
visualize an atom subset using the integrated selection tool. The calculated
property can be saved in a file and/or showed in the included graph editor.
VEGA is available for free at theURL:
Best regards


> Dear sir,
> I want to get a figure of "bond distance vs time" with VMD. In VMD
> this can be done by select the two atoms you want to calculate the
distance for.
> However I think the system(such as protein) is always very large, it is
> to find and click the atoms accurately and easily. Whether has someone
> way to realize it?
> Or, I think we can write a small script just like namdplot which can
plot the
> figure of energy, temperature and others vs time. Do someone have this
kind of
> script?
> I am looking forward to your reply!

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