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

2016-05-15 Thread sun 
You can convert xpm2txt and plot in Origin as well

Sent from my iPhone

> On 29-Jan-2014, at 11:21 am, tarak karmakar  wrote:
> 
> 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 
> 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 
>> National Yang-Ming University<
>> http://nymu-e.web.ym.edu.tw/front/bin/home.phtml>
>> Taipei, Taiwan
>> mon.123c...@gmail.com
>> +886-981702268
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
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[gmx-users] How to visualize the Free Energy Landscape file generated by g_sham

2014-01-28 Thread Monoj Mon Kalita 
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 
Biophotonicshttp://www.ym.edu.tw/biophotonics/eng_version/home.htm
Fischer's Lab http://www.ym.edu.tw/~wfischer/group.html
National Yang-Ming Universityhttp://nymu-e.web.ym.edu.tw/front/bin/home.phtml
Taipei, Taiwan
mon.123c...@gmail.com
+886-981702268
-- 
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Re: [gmx-users] How to visualize the Free Energy Landscape file generated by g_sham

2014-01-28 Thread 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.123c...@gmail.comwrote:

 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.123c...@gmail.com
 +886-981702268
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.

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