[gmx-users] How to visualize the Free Energy Landscape file generated by g_sham

[tarak karmakar]

Hi Monoj,

You can use GNU 3D plot for this particular case.

cheers,
Tarak


On Wed, Jan 29, 2014 at 8:02 AM, Monoj Mon Kalita <mon.123chem at gmail.com>wrote:

> Dear Gromacs user,
>
> I have used the g_sham method to generate free-energy-landscape.xpm file.
> To do that I have followed this website
>
> http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html
>
> Now my problem is how to plot RMSD, radius of gyration and free energy in a
> single file . I can have a plot of Rg and RMSD in 2D, but unable to plot
> Rg, RMSD and Free energy value in a single file as they have shown in the
> website. I have used the mathematica software version 9 and have used the
> notepad given by the website. When I execute the program it doesn't show
> any output. Is there any other way to have a nice plot of Rg, RMSD and Free
> energy together in a single polt? Have a nice day.
>
> --
>
>  With Regards
> Monoj Mon Kalita
> Institute of Biophotonics<
> http://www.ym.edu.tw/biophotonics/eng_version/home.htm>
> Fischer's Lab <http://www.ym.edu.tw/~wfischer/group.html>
> National Yang-Ming University<
> http://nymu-e.web.ym.edu.tw/front/bin/home.phtml>
> Taipei, Taiwan
> mon.123chem at gmail.com
> +886-981702268
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