[gmx-users] 3Dplot

Alessandro Casoni alessandro.casoni at unimi.it
Wed Feb 4 10:27:00 CET 2009

David van der Spoel ha scritto:
> Alessandro Casoni wrote:
>> Dear gmx-users,
>> i would like to generate a 3D plot of my potential energy/RMSD/radius 
>> of gyration.
>> I used g_energy, g_rms and g_gyrate to collect informations on my 
>> simulation..any suggestion on software able to generate 3D plot?
> Please check
>  Marvin Seibert, Alexandra Patriksson, Berk Hess and David van der 
> Spoel: Reproducible polypeptide folding and structure prediction using 
> molecular dynamics simulations J. Mol. Biol. 354 pp. 173-183 (2005)
> We used g_sham to combine the data and Visit (visit.llnl.gov) for the 
> 3D plots. The software has evolved since then obviously, so you can 
> probably make it (even) prettier now. An alternative is gnuplot.
>> thanks
>> alessandro
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thank you David,

you probably solved my problems....

g_sham to combine the data?
for example g_sham -f energy.xvg -f rmsd.xvg -f gyrate.xvg ?
and output?


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