[gmx-users] secondary structure

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 10 15:58:48 CEST 2008

s lal badshah wrote:
> Hi All,
> I want to study and calculate the secondary structure as a function of 
> time of my MD simulated protein. I have no DSSP installed but will use 
> VMD for this.Can any one suggest me which files of MD simulation output 
> I should used? or I need to develop PDB file of the whole MD simulation 
> trajectories?

VMD reads any GROMACS-format trajectory natively into a suitable 
structure file, e.g. the .gro file produced by your simulation. 
Searching the wiki to find http://wiki.gromacs.org/index.php/VMD would 
have told you this. Anyway, then do whatever you like with VMD from there.


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