[gmx-users] protein ligand tutorial

Albert mailmd2011 at gmail.com
Mon Jan 20 15:17:07 CET 2014


I noticed that in the tutorial ligand Gromacs tutorial, there is a 
setting in .mdp file like:

energygrps:  protein ligand

in order to claculate the interactions between protein/ligand by g_lie.

I am just wondering, would it be better to include the solvent to 
evalutate the protein ligand interactions and create energy group like:

energygrps: protein_water_ions ligand ?

thank you very much.


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