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

[Mark Abraham]

On 28/07/2012 4:49 PM, Rajitha Tatikonda wrote:
> Hi,
>
> 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)).

So the 
http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups 
won't be suitable and you'll have to make some custom groups in your 
http://www.gromacs.org/Documentation/File_Formats/Index_File

Mark