88 lines
3.4 KiB
Plaintext
88 lines
3.4 KiB
Plaintext
Ethane to Methanol in Water
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===========================
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Example calculation of the difference in free energy of hydration upon
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transforming ethane into methanol with LAMMPS using *compute fep* and
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*fix adapt/fep*.
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Ethane and methanol are represented by the OPLS-AA force field (1
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molecule). Water is represented by the 3-site SPC/E model (360
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molecules).
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The strategy used to perform the alchemical transformation is the
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following:
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* The dual topology approach is used, therefore all the atoms of
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ethane and methanol are present throughout the simulation, only some
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of them are dummy sites at the endpoints of the
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transformation. Masses and intramolecular terms (bond lengths,
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angles, dihedrals) are not changed.
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* Interactions of sites that are being created (from dummy sites) or
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deleted (to become dummy sites) are treated using soft-core verions
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of the Lennard-Jones and Coulomb potentials (*pair
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lj/cut/coul/long/soft*) in order to avoid singularities. The
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exponent of the coupling parameter lambda in the soft-core pair
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potentials was in this example n = 1.
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* Eletrostatic charges that are modified are varied linearly from the
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initial to the final values. This keeps the overall charge of the
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molecule constant, which is good for the long range electrostatics
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(the coupling parameter lambda has no effect on the kspace terms).
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The following directories contain input files and results for
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calculations using free-energy perturbation (FEP), thermodynamic
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integration (TI/FDTI) and Bennet's acceptance ratio methods:
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* `mols` -- Molcule description files and force field database used to
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create the initial configurations for the simulations `data.0.lmp`
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and `data.1.lmp`
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* `fep01` -- Calculation using FEP, multi-stage transformation of an
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ethane molecule into methanol. Results in `fep01.lmp`
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* `fep10` -- Calculation using FEP, multi-stage transformation of a
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methanol molecule into ethane. Results in `fep10.lmp`
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* `fdti01` -- Calculation using FDTI, transformation of an
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ethane molecule into methanol. Results in `fdti01.lmp`
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* `fdti10` -- Calculation using FDTI, transformation of a
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methanol molecule into ethane. Results in `fdti10.lmp`
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* `bar01` -- Calculation using BAR, 1-step transformation of an
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ethane molecule into methanol. Results in `bar01.lmp`
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* `bar10` -- Calculation using BAR, 1-step transformation of a
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methanol molecule into ethane. Results in `bar10.lmp`
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The free-energy profiles can be observed by plotting the values in the
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third column of the results files. The Python scripts `fep.py`,
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`nti.py`, `fdti.py`, and `bar.py` found in the `tools` directory can
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be used to calculate the free-energy differences corresponding to the
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above transformations:
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fep.py 300 < fep01.lmp
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fep.py 300 < fep10.lmp
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nti.py 300 0.002 < fdti01.lmp
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nti.py 300 0.002 < fdti10.lmp
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fdti.py 300 0.002 < fdti01.lmp
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fdti.py 300 0.002 < fdti10.lmp
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bar.py 300 bar01.lmp bar10.lmp
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The outputs are in kcal/mol and can be compared with the experimental
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value of -6.93 kcal/mol and with simulation value from the literature:
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-6.7 kcal/mol [Jorgensen, Ravimohan, J Chem Phys 83 (1985) 3050], -6.8
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kcal/mol [Goette, Grubmüller, J Comp Chem 30 (2007) 447].
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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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