This is a problem of sampling. The number of classical states of an N-body system grows with O( 3 ^ N ). To sample this space, advanced techniques are required. Replica Exchange (RE), also known as parallel tempering, is an example that uses parallelization, and Hamiltonian Replica Exchange is a subset of RE that scales the energy of the replicas. The number of simulations required grows at O( N^(1/2) ), where N is number of atoms in the system. Replica Exchange with Dynamical Scaling (REDS) attempts to address this problem to decrease computational cost. It has been shown to increase efficiency 10-fold. We implemented REDS in GROMACS 2018. (Abraham 2015)
All changes to the source code were written in the form of parallel methods. Scripts were written in Python and Perl to automate the experiment entirely. An exchange connects a region of high energy space, far above the surface of the landscape, to low energy space, which approaches the surface of the landscape, which represents the natural conformational progression of the molecule. Using REDS we were able to achieve exchanges at temperatures spaced too far apart to exchange using normal RE. Ergo, the flexibility of dynamical scaling allowed regions of phase space that would have gone unsampled to be mapped, addressing our initial problem of sampling.
| Identifer | oai:union.ndltd.org:uno.edu/oai:scholarworks.uno.edu:honors_theses-1117 |
| Date | 01 May 2018 |
| Creators | Schwing, Gregory John |
| Publisher | ScholarWorks@UNO |
| Source Sets | University of New Orleans |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | Senior Honors Theses |
| Rights | http://creativecommons.org/licenses/by/4.0/ |
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