[gmx-users] Analysis of a simulation

sukesh chandra gain sukesh at atc.tcs.com
Tue Feb 16 06:42:28 CET 2010

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 

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.


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

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