[gmx-users] Analysis of a simulation

Saikat Banerjee banskt.saikat at gmail.com
Tue Feb 16 10:38:22 CET 2010

On Tue, Feb 16, 2010 at 11:12 AM, sukesh chandra gain <sukesh at atc.tcs.com>wrote:

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

Please have a look at the g_ tools.

make a proper index file according to your needs using make_ndx or you can
do it manually also.

Have a look at Gromacs manual. Chapter 8.

> 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"  ?

try g_hbond, g_saltbr depending on your system... you may look at other

> 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.

g_rms, g_rmsdist

> 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).
g_saltbr after converting trajectory with trjorder.

> 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
> --
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Saikat Banerjee
Integrated Ph.D student
Prof B. Bagchi's group
Room no. 210
Solid State and Structural Chemistry Unit (SSCU)
Indian Institute of Science
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