Difference between revisions of "Tutorials"
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== NAMD Tutorials == | == NAMD Tutorials == | ||
| − | [ 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 a naked Lennard-Jones particle into a sodium ion. Next, the variation in solvation free energy upon mutation of a tyrosine residue into alanine is examined in the Ala–Tyr–Ala tripeptide. Last, the concept of standard binding free energy is illustrated in the simple case of a potassium ion binding a ionophore, 18–crown–6 | + | [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 a naked Lennard-Jones particle into a sodium ion. Next, the variation in solvation free energy upon mutation of a tyrosine residue into alanine is examined in the Ala–Tyr–Ala tripeptide. Last, the concept of standard binding free energy is illustrated in the simple case of a potassium ion binding a ionophore, 18–crown–6 |
Revision as of 12:43, 10 July 2013
GROMACS Tutorials
A very useful tutorial for calculating free energies in GROMACS 4.5.3 by Justin Lemkul.
For tutorial for earlier versions of Gromacs, see our original tutorial on methane insertion in water.
For tutorials for 4.6.2 versions of GROMACS, see instructions on how to run this calculation with GROMACS 4.6 using standard free energy calculations, or using using expanded ensemble simulations.
AMBER Tutorials
An AMBER tutorial for free energy calculations.
CHARMM Tutorials
NAMD Tutorials
A tutorial for setting up free energy calculations using NAMD. Specific problems include computing the free energy of charging a naked Lennard-Jones particle into a sodium ion. Next, the variation in solvation free energy upon mutation of a tyrosine residue into alanine is examined in the Ala–Tyr–Ala tripeptide. Last, the concept of standard binding free energy is illustrated in the simple case of a potassium ion binding a ionophore, 18–crown–6