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Could you please point me to the papers you have implemented the free energy from?
There is now a free energy plugin for OpenMM, which supports alchemical free energy calculations at the library level. (I don't believe the gromacs interface supports this yet.)
The adaptive biasing force (ABF) method can conceivably already be implemented using the CustomNonbondedForce, CustomBondedForce, and/or CustomExternalForce classes, depending on the coordinate along which you wish to compute the potential of mean force.
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SimTK is maintained through Grant R01GM124443 01A1 from the National Institutes of Health (NIH). It was initially developed as part of the Simbios project funded by the NIH as part of the NIH Roadmap for Medical Research, Grant U54 GM072970.