[gmx-users] energy-grps specification in mdp -regd

Rajitha Tatikonda sairam.tatikonda at gmail.com
Sat Jul 28 08:49:31 CEST 2012


I am intending to calculate binding affinity using Linear Interaction
method (LIE method) for which I need to perform two simulations for
given ligand both in free and bound states and get the values of
Electrostatic and Van der Waals Interaction energies of the ligand.
I have done simulation of free state of ligand. As Peptide (Chain C)
of complex is the ligand, I could not understand how this is to be
specified under energy-grps option in mdp for my system (as it is done
in protein -ligand complex gromacs tutorial by specifying protein,
JZ4(name of the ligand)).

Any help will be highly appreciated.

Thanks in advance.


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