I have been trying to understand the Implicit Ligand Sampling (ILS) using VMD/NAMD to understand and study oxygen tunnels in the protein of interest and I have all the parameter files and all the respective files to start the simulation. I see there are a few ways to run this simulation, one by VMD interface ( VMD -> Analysis -> Implicit Ligand Sampling ) and another by using volmap utils. I tried both of them but no progress though.
I did try these commands in VMD Tk console
volmap ils 0 {{-36.772789001464844 -34.06757354736328 -109.6866226196289} {41.513118743896484 51.53120422363281 14.332422256469727}} -probesel [atomselect top "resname O2"] -o ils.dx
It works fine but I am not getting the output that I am interested in, I would like to have free energy map of O2 ( G(r) kcal/mol vs Channel coordinate r/A).
I will be happy to have a discussion with you.