[gmx-users] Linear Interaction energy calculations

[sai nitin]

Dear all,

I recently started protein ligand simulation using gromacs my aim is
to calculate binding free energies after simulations...I adapted
justin tutorial
and  done 10 ns MD simulations using CHARMM FF and now going through
LIE (Linear Interaction Energie method) g_lie in gromacs..

And came across that to perform LIE using gromacs involves two MD
simulations one with protein - ligand simulation in solvent (which i
finished)..and another with ligand only in solution in this step i got
stuck can any body tell or suggest some tutorials to perform MD
simulations for only ligand

Thanks in advance

--

Sainitin D