From: mish (
Date: Tue Jul 07 2015 - 12:12:29 CDT

Dear all,

Is possible to calculate volume of the space sampled by ligand in MD
simulation, either from Amber trajectory or by loading multiple PDB files
of ligand ( PDB of each conformation of ligand extracted from simulation) ?

In brief, I have an octahedral simulation box, where I am simulation
binding/unbinding of ligand from a protein. I need to calculate total
volume of the system (protein+ligand+water) and total volume accessed my
ligand (within the simulation box) during the MD simulation.