[gmx-users] Analysis

[RAHUL SURESH]

I have few doubts in MD analysis.

*How to calculate the deviation angle between two helix of a protein? (for
every ns) or in other words how can I know whether the two helices
(consecutive)
 have moved apart during simulation?

*In saltbridge analysis how can I eliminate CL and NA ions? (Before the
analysis)

PS:- Its Protein-Ligand complex simulated for  100ns.

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*