Constant pH Simulations in GROMACS with FMM Electrostatics
The protonation state of most biomolecules is not static, but changes stochastically with time according to the pH of the surrounding solution. For some biomolecules, pH-induced protonation changes are an essential part of their function. However, a typical MD simulation does not include protonation dynamics, but simply uses fixed protonation states that are likely at the given pH. To overcome this limitation and make biomolecular simulations more realistic, we are developing a constant pH simulation protocol based on lambda dynamics and FMM electrostatics.
GROMACS constant pH documentation, download and install instructions
Please follow this link for comprehensive documentation on how to set up constant pH simulations with FMM electrostatics in GROMACS.
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