I did a coarse grained simulation with martini parameters using Gromacs 5.0. Followed this: http://cgmartini.nl
My simulation is done. But when I open the trajectory in VMD, I can see it only as beads. Not secondary structures or lines.
Can anyone provide a detailed procedure of how to implement the .tcl scripts to get the secondary structure and stick representations for the frames?
Thanks.
Try the Bendix plugin:
http://sbcb.bioch.ox.ac.uk/Bendix/index.html
Also, have a look at the following pages:
http://cgmartini.nl/index.php/tutorials-general-introduction/cgviz
http://cgmartini.nl/index.php/rb
http://md.chem.rug.nl/index.php/tools2/visualization
VMD can not understand either the atoms or the bonds between them unless you give it a topology data.
VMD can't extract the secondary structure from just the CG model. Try this: http://cgmartini.nl/index.php/rb
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