Q-RepEx is an open source tool designed to perform replica exchange simulations with Q6. The idea is adapted from "H. Liu, A. Warshel, The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies, Biochemistry 46 (20) (2007) 6011–6025. doi:10.1021/bi700201w". The procedure accelerates sampling by parallelising the FEP/US process and improves statistics by increased sampling. The python script, Q-RepEx, main functionality is the unconditional exchange of simulation conditions for a series of FEP/US simulations.
- Python
- git (optional)
Qrepex is relying on Q6 which is free and opensource software licensed under the GPL v2.
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Q: https://github.com/qusers/Q6
Download and compile Q. Optionally install to $PATH.
We recommend using git to download Q-Repex, so that future releases of Q-Repex are easily accessible.
Here the suggested steps:
Clone into Q-Repex:
git clone https://github.com/kamerlinlab/Qrepex qrepex
The user provided input for Q-RepEx is purposely short in order to ease functionality. An example input is shown below:
python repex v1.X.py fep 10 5
repex v1.X.py is the name of the current version of Q-RepEx, fep is the base filename, 10 is the number of US windows and 5 is the number of consecutive runs to be performed. The base filename has to be used for the input, output, trajectory, restart and energy files. A help module is provided in Q-RepEx. It can be activated by issuing:
python repex v0.3.py help
The development of Q-RepEx is mainly funded by academic research grants. To help us fund development, we humbly ask that you cite the Q-RepEx paper:
- Q-RepEx: A python pipeline to increase sampling of EVB simulations
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