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Hi everyone,
I trained a GAP for SiO2. It seems to work reasonably well in MDs, but the errors I find in testing datasets are quite high. Moreover, there seems to be a fix offset in the energy e…
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### Describe the bug
I am trying to fit a custom spectrum which has spectral data below 1 keV (though not usable). I am trying to fit the spectra with above 1 keV using `spec.energy_fitting_range` at…
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This is basically the same as https://github.com/OpenFreeEnergy/openfe/issues/809 except there may be complications in the hocus pocus of free energy magic and custom forces that makes this harder or …
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It would be useful to have an analysis module that generates useful plots for diagnosing "simulation health", like [the one in yank ](https://github.com/choderalab/yank/blob/master/Yank/reports/YANK_H…
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### Team Name: edelweiss
@jeungrac @jyryu98 @Eyuel-E
### Project Description:
Variational Quantum Eigensolvers (VQE) for calculating ground state energies of molecules are one of the major …
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[Hou, Tingjun, Junmei Wang, Youyong Li, and Wei Wang. “Assessing the Performance of the Molecular Mechanics/Poisson Boltzmann Surface Area and Molecular Mechanics/Generalized Born Surface Area Methods…
cramg updated
3 years ago
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cramg updated
3 years ago
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Right now, we subtract the mean calculated ΔG and mean experimental ΔG and plot, making for a ridiculous plot that include ΔG >= 0 (Kd > 1 Molar), which is totally nonsensical for an absolute ΔG.
!…
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## Motivation
Membrane-protein systems account for ~ 60% of possible target space. Being able to calculate binding free energies for membrane-containing systems would be a significant advantage.
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During the rerun step, `gmx mdrun -rerun` is used to obtain potential energies of each of the sampled conformations of the system using every hamiltonian. During this process, if the potential energy …