Add report description of restraint
"cell_type": "markdown",
"metadata": {},
"source": [
- "# Restraint energies and distances distribution\n",
+ "# Radially-symmetric restraint energy and distance distributions\n",
"\n",
- "When unbiasing the restraint, it is important"
+ "This plot is generated only if the simulation employs a radially-symmetric restraint (e.g. harmonic, flat-bottom), and the unbias_restraint option of the analyzer was set.\n",
+ "\n",
+ "## What do I want to see here?\n",
+ "When unbiasing the restraint, it is important to verify that the cutoffs do not remove too many configurations sampled from the bound state. Almost all the density of the bound state should be on the left of an eventual cutoff (red line).\n",
+ "\n",
+ "In general, we expect the distribution in the bound state to be narrower than in the non-interacting state. If this is not the case, then either the binder is weak and it has left the binding site during the simulation, or the restraint might be too tight and limiting the conformational space explored by the ligand."
]
},
{
"metadata": {},
"outputs": [],
"source": [
- ""
+ "restraint_distribution_figure = report.restraint_distributions_plot()"
]
},
{
