protocols

This repo contains a collection of protocols useful for carrying out different types of computational-chemistry simulations.

MD (Molecular Dynamics)

cMD (Conventional MD)

• create_md.sh: Bash script for creating all files and folders required for carrying out conventional MD simulations, including the preproduction step. Further information can be found in the comments inside the script.

aMD (Accelerated MD)

• aMD_energy_reweighting.sh: Bash script that assists the energy rewighting of an aMD using the PyRewighting package from MiaoLab. Further information can be found in the script.

GaMD (Gaussian accelerated MD)

• GaMD_equilibration_nvt.mdin & GaMD_equilibration_npt_semiisotropic.mdin: AMBER inputs for running GaMD equilibration in NVT and semiisotropic NPT conditions.
• GaMD_production_nvt.mdin & GaMD_production_npt_semiisotropic.mdin: AMBER inputs for running GaMD production in NVT and semiisotropic NPT conditions.

sMD (Steered MD)

• smd_setup.py: Python script for setting up a sMD simulation.
• pmf_from_smd.py: Python script for calculating PMF from several sMD simulations.

MM-PBSA - Molecular Mechanics Poisson-Boltzmann Surface Area

• mmpbsa_setup.sh: Bash script for creation of topology files of complex, receptor and ligand (ante-MMPBSA), and calculation of PB Binding energies of a ligand bind inside a receptor.
• entropy.sh: Bash script for calculation from MM-PBSA results entropy correction of the binding energy.