Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 13, Issue 12, Pages 6373-6381Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.7b00738
Keywords
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Funding
- EPSRC
- NIH
- Memorial Sloan Kettering Cancer Center, NIH [P30 CA008748]
- EPSRC [EP/J010189/1, EP/L015722/1, EP/G03690X/1]
- Royal Society Wolfson Research Merit Award
- EPSRC [EP/J010189/1] Funding Source: UKRI
- Engineering and Physical Sciences Research Council [1515432, EP/J010189/1, 976841] Funding Source: researchfish
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The ability of grand canonical Monte Carlo (GCMC) to create and annihilate molecules in a given region greatly aids the identification of water sites and water binding free energies in protein cavities. However, acceptance rates without the application of biased moves can be low, resulting in large variations in the observed water occupancies. Here, we show that replica-exchange of the chemical potential significantly reduces the variance of the GCMC data. This improvement comes at a negligible increase in computational expense when simulations comprise of runs at different chemical potentials. Replica-exchange GCMC is also found to energies as calculated with grand canonical integration, which has substantially increase the precision of water binding free allowed us to address a missing standard state correction.
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