Difference between revisions of "Tutorials"
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| + | {{Free Energy Howto}} | ||
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| + | Included below are a number of free energy tutorials for a variety of molecular programs. They do not necessarily all follow all of the guidelines outlined, but have generally been prepared by advanced users of the relevant codes, so should work with the. Please direct questions about the tutorials that are not hosted on Alchemistry.org to the authors of the tutorials themselves! | ||
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== GROMACS Tutorials == | == GROMACS Tutorials == | ||
[http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html A very useful tutorial] for calculating free energies in [http://www.gromacs.org GROMACS] 4.5.3 by Justin Lemkul. | [http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html A very useful tutorial] for calculating free energies in [http://www.gromacs.org GROMACS] 4.5.3 by Justin Lemkul. | ||
| − | For tutorial for earlier versions of Gromacs, see our original tutorial on [http://www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial methane insertion in water]. | + | <!--For tutorial for earlier versions of Gromacs, see our original tutorial on [http://www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial methane insertion in water].--> |
| − | For tutorials for 4.6. | + | For tutorials for 4.6.3 and later versions of GROMACS, see [[GROMACS 4.6 example: Direct ethanol solvation free energy|instructions]] on how to compute ethanol solvation free energy using standard free energy calculations and Hamiltonian replica exchange, or [[GROMACS 4.6 example: Ethanol solvation with expanded ensemble|using expanded ensemble simulations]]. |
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| + | A tutorial for absolute binding free energy calculations with GROMACS 2016 is instead found [[Absolute Binding Free Energy - Gromacs 2016|here]]. | ||
== AMBER Tutorials == | == AMBER Tutorials == | ||
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[http://ambermd.org/tutorials/advanced/tutorial9/ An AMBER tutorial for free energy calculations]. This tutorial describes setting up and running free energy calculations of benzene and phenol to the T4 Lysozyme L99A model protein. | [http://ambermd.org/tutorials/advanced/tutorial9/ An AMBER tutorial for free energy calculations]. This tutorial describes setting up and running free energy calculations of benzene and phenol to the T4 Lysozyme L99A model protein. | ||
| − | + | [http://ringo.ams.sunysb.edu/index.php/AMBER_TI_Tutorials A similar tutorial adapted for Amber10]. | |
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== NAMD Tutorials == | == NAMD Tutorials == | ||
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[http://www.ks.uiuc.edu/Training/Tutorials/namd/FEP/tutorial-FEP.pdf A tutorial for setting up free energy calculations using NAMD]. | [http://www.ks.uiuc.edu/Training/Tutorials/namd/FEP/tutorial-FEP.pdf A tutorial for setting up free energy calculations using NAMD]. | ||
| − | Specific problems include computing the free energy of charging | + | Specific problems include computing the free energy of charging Lennard-Jones particle to produce a sodium ion, computing the relative free energy of mutation of a tyrosine residue into alanine is in the Ala–Tyr–Ala tripeptide, and computing the binding free energy of a potassium ion to a ionophore, 18–crown–6 ether. |
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| + | [http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf A tutorial for Protein-ligand binding with NAMD]. | ||
| + | It specifically examines the binding of a small, proline-rich peptide, referred to as p41, associating to the Src homology 3 domain of a | ||
| + | tyrosine kinase. | ||
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| + | == CHARMM Tutorials == | ||
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| + | We're looking for a good CHARMM tutorial! Care to recommend one? | ||
Latest revision as of 07:29, 23 March 2017
| Free Energy How-to's |
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 |
Included below are a number of free energy tutorials for a variety of molecular programs. They do not necessarily all follow all of the guidelines outlined, but have generally been prepared by advanced users of the relevant codes, so should work with the. Please direct questions about the tutorials that are not hosted on Alchemistry.org to the authors of the tutorials themselves!
GROMACS Tutorials
A very useful tutorial for calculating free energies in GROMACS 4.5.3 by Justin Lemkul.
For tutorials for 4.6.3 and later versions of GROMACS, see instructions on how to compute ethanol solvation free energy using standard free energy calculations and Hamiltonian replica exchange, or using expanded ensemble simulations.
A tutorial for absolute binding free energy calculations with GROMACS 2016 is instead found here.
AMBER Tutorials
An AMBER tutorial for free energy calculations. This tutorial describes setting up and running free energy calculations of benzene and phenol to the T4 Lysozyme L99A model protein.
A similar tutorial adapted for Amber10.
NAMD Tutorials
A tutorial for setting up free energy calculations using NAMD.
Specific problems include computing the free energy of charging Lennard-Jones particle to produce a sodium ion, computing the relative free energy of mutation of a tyrosine residue into alanine is in the Ala–Tyr–Ala tripeptide, and computing the binding free energy of a potassium ion to a ionophore, 18–crown–6 ether.
A tutorial for Protein-ligand binding with NAMD. It specifically examines the binding of a small, proline-rich peptide, referred to as p41, associating to the Src homology 3 domain of a tyrosine kinase.
CHARMM Tutorials
We're looking for a good CHARMM tutorial! Care to recommend one?