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
_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


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?

alessandro
_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to