[gmx-users] Regarding simulation analysis and free energy calculation

rama david ramadavidgroup at gmail.com
Sun Aug 10 09:56:54 CEST 2014

Dear users,
                   I did the docking of peptide and receptor in Vina
further I decided to do the simulation in gromacs. 4.5.5 version for 10ns.
after this I made the energygroups in mdp file for ligand and and receptor.
I also make the appropriate changes in index file. I rerun the above
simulation again.

Now I want to do the following analysis . I will be thankful if you suggest
how to do analysis  and suggestion .

1.  I want to calculate the hydrogen bond --- I used g_hbond.

2. Now I want to find the interaction energy of ligand and receptor .
   How to do that ???

3. Is it possible to calculate free enegy of interaction between ligand and
receptor ?
    how to do this ?

4. I want to make the graph with respect to free energy surface  and
     conformation.? How to do this ?

I will be very thankful for your help. I am eagerly waiting for
your kind words.

With Best wishes,
Rama David

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