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Folding and Binding of DPO4

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Description: This repository includes: (1) necessary files for setting up and running Gromacs (version 4.5.7 with PLUMED version 2.5.0) simulations on DPO4 folding and DNA-binding with coarse-grained structure-based models. (2) programs and scripts for performing WHAM and reweigthing WHAM for DPO4 REMD folding (3) programs and scripts for performing DPO4 kinetic folding simulations (4) programs and scripts for performing WHAM for DPO4-DNA umbrella sampling binding (5) programs and scripts for performing frequency-adaptive metadynamics (rate calculation matlab script can be found at JCTC, 2014, 10, 1420-1425) Please let me know if you have any questions

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