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revised October 21, 2014
The LEWIS model unpacks molecules into atomic kernels and valence electron pairs, much as in the dot diagrams taught in General Chemistry. These particles interact pairwise via potentials that incorporate quantum features, in particular the diffuse nature of the electron distribution around the particle coordinates. The pseudo-classical nature of the model and the restriction to pairwise interactions makes simulations very efficient, allowing large samples and long trajectories.
| GROMACS tables and templates for LEWIS water by Seyit Kale |
When you use LEWIS, please cite:
Seyit Kale & Judith Herzfeld (2012).
Natural Polarizability and Flexibility via Explicit Valency: The Case of Water.
J. Chem. Phys. 136:084109.
Seyit Kale & Judith Herzfeld (2012).
Proton Defect Solvation and Dynamics in Aqueous Acid and Base.
Angew. Chem. Int. Ed. 124:11191.
Included are three folders:
lewis_template_neutral,
lewis_template_deprotonated, and
lewis_template_protonated.
Templates include the required Gromacs files for energy minimizing and running
NPT-ensemble MD simulations of 500 monomers of LEWIS water in a cubic box.
The neutral case includes 500 water molecules, the protonated 499 waters and 1 hydronium,
and the deprotonated 499 waters and 1 hydroxide.
To run the NVT ensemble, energy minimize the system and equilibrate the density via
NPT, then set the barostat option to "None". For NVE, also set the thermostat
to "None".
The LEWIS potentials here are introduced as user-defined tabulated potentials. These
tables can be found under lewis_template_neutral. The other two folders only include
files that differ from the neutral case.
We recommend first running the neutral water box. To run LEWIS, go to this
directory and modify rungmx.sh. If you have compiled GROMACS via MPI, set
mpi_present to 1 and specify the number of available CPU cores in your system.
Then type: bash ./rungmx.sh
Alternatively, you can copy and paste the grumpp and mdrun commands in rungmx.sh
into your terminal window.
To run protonated and deprotonated cases, copy both grompp files and all six
table files inside the neutral case folder into the protonated and deprotonated
case folders, then follow the prior step above.
This software is provided "as is", and you cannot re-distribute it. The authors make no warranties, either express or implied, as to any matter whatsoever with respect to the software. In no event will the authors be liable for any loss of profits, or any incidental, special, exemplary, or consequential damages of any nature whatsoever, arising out of or relating to the use or performance of the software.
If you have any comments, suggestions, concerns or questions, please contact us.