From: Payman Pirzadeh (
Date: Tue May 14 2013 - 19:38:23 CDT

I am running VMD 1.9.1 on Linux Ubuntu 12.10. I run my simulations with
GROMACS 4.5.4, and I upload the .gro and .xtc file in VMD to perform PCA
analysis. I use the default NMWiz1.0 plugin. When the PCA analysis is
done and the information is loaded, things get strange. For instance, I
cannot change the protein presentation into new cartoon despite
calculating the components for the backbone! If I change the
presentation from backbone to CA, then arrows disappear, or even
sometime the whole structure disappears and never reappear. The
selection and redrawing, in particular, appear to be not working well. I
found the online instructions not easy to follow. Are there any links or
documentation with appropriate instructions/trouble shooting available
on NMWiz?
Thanks for your help.