59 lines
2.2 KiB
Markdown
59 lines
2.2 KiB
Markdown
Free Energy of Hydration of Methane
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===================================
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Example calculation of the free energy of hydration of methane with
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LAMMPS using *compute fep*, *fix adapt/fep* and *pair lj/cut/coul/long/soft*.
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Methane is represented by the 5-site OPLS-AA model (1 molecule). Water
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is represented by the 4-site TIP4P-Ew model (360 molecules). Interactions
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of sites that are being created or deleted are treated using Lennard-Jones
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and Coulomb potentials with soft cores (*pair lj/cut/coul/long/soft*)
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in order to avoid singularities. Trajectories are at constant NpT, so
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corrections for the fluctuating volume are included.
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The following directories contain input files and results for
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calculations using free-energy perturbation (FEP) and
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finite-difference thermodynamic integration (FDTI):
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* `mols` -- molecule description files and force field database used
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to create the initial configuration used for the simulations
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`data.lmp`
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* `fep01` -- Calculation using FEP, multi-stage creation of a methane
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molecule. Results in `fep01.fep`
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* `fep10` -- Calculation using FEP, multi-stage deletion of a methane
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molecule. Results in `fep10.fep`
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* `fdti01` -- Calculation using TI/FDTI, creation of a methane
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molecule. Results in `fdti01.fep`
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* `fdti10` -- Calculation using TI/FDTI, deletion a methane
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molecule. Results in `fdti10.fep`
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The Python scripts `fep.py`, `fdti.py` and `fti.py` found in the
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`tools` directory can be used to calculate the free-energy differences
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corresponding to the transformations above:
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fep.py 300 < fep01.fep
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fep.py 300 < fep10.fep
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fdti.py 300 0.002 < fdti01.fep
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fdti.py 300 0.002 < fdti10.fep
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nti.py 300 0.002 < fdti01.fep
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nti.py 300 0.002 < fdti10.fep
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The outputs are in kcal/mol and can be compared with the experimental
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value of 2.0 kcal/mol, or with a simulation value from the literature
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obtained with the same force field models used here: 2.27 kcal/mol
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[MR Shirts, VS Pande, J Chem Phys 122 (2005) 134508](https://doi.org/10.1063/1.1877132).
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These example calculations are for tutorial purposes only. The results
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may not be of research quality (not enough sampling, size of the step
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in lambda or of the delta for numerical derivative not optimized, no
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evaluation of ideal-gas contributions, etc.)
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