[gmx-users] Analysis of a simulation

[sukesh chandra gain]

Dear All,

It is not clear from manual how to analyse my requirements after simulation.
Could you please help me in the following regards:

1> How to get the graph on "occupancy of hydrogen bond interactions of 
ligands throughout 5 ns simulation" and "occupancy of a particular 
salt-bridge throughout the simulation"  ?

2> I want to get a graph of the distances of some particular co-factor 
atoms and active site residues atoms throughout the simulation.
Suppose I want the distance graph between DPM:C9B and Arg7:CA for total 
simulation.

3> Average hydrogen bond distance between active site residues and ligand.

4> RMSD of some particular residues from its initial structure.

5> Total formal charge residing at active site  throughout the 
simulation (All +vely charge and -vely charge residues within 15 A 
radius of active site will be considered).

It would be a great help if you could kindly give some sample commands  
for these analysis.

Sorry for lots of questions.

Thank You.

Regards,
Sukesh


-- 
Sukesh Chandra Gain
TCS Innovation Labs
Tata Consultancy Services Ltd.
'Deccan Park', Madhapur
Hyderabad 500081
Phone:  +91 40 6667 3572