ACEMDtk: ACEMD toolkit protocols

Copyright Universitat Pompeu Fabra 2012. All rights reserved.
It is forbidden to copy this material in any form. If you are interested in the content of these pages please just link them directly.

ACEMDtk is a series of protocol sheets with best methods to perform certain common actions when you run molecular dynamics simulations. It goes from simple tasks on equilibrating the proteins to more advanced protocols to compute free energies.

  • ACETK.PRMAMBER: Molecule parametrization using the Amber force field

  • ACETK.PRMCHARMM: Molecule parametrization using the Charmm force field

  • ACETK.BLDAMBER: Build a globular protein with the Amber force-field (NEW!)

  • ACETK.BLDCHARMM: Build a globular protein with the Charmm force-field

  • ACETK.BLDMEMBPROT: Build a membrane protein system

  • ACETK.EQ: Equilibrate a globular protein in solution

  • ACETK.SMD: Protein-ligand binding affinity estimation using steered molecular dynamics (NEW!)

  • ACETK.BINDUS: Protein-ligand binding affinity calculations by umbrella sampling (restricted access)

  • ACETK.METADYN: Metadynamics free energy calculation using PLUMED (Coming soon)

ACETK protocol naming convention. Each protocol is named accordingly to the following scheme: 

 "PROTOCOL SET".PROTOCOL NAME"."PROTOCOL VERSION NUMBER"

To report the protocol used in a paper, please use the naming convention. For instance: "The molecular system was equilibrated using protocol ACEMDTK.EQ.v1 (http://multiscalelab.org/acemd/protocols/ACETK.EQ).

Background information

Copyright 2008-2011. All rights reserved.