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Hi all,
I am mutating a residue of a protein using TI in AMBER, and outputting at the same time the MBAR data. In the end, I am using alchemical_analysis, but I have a problem. I know that usually fo…
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Hi,
I'm training a model with 1000 configurations of pure water taken at different densities generated from DFT calculations (VASP) at 300K.
I am using the following parameters for training:
…
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I'm looking at the oxidation of CO on Pd(100). I am using as my two descriptors the binding energy of carbon monoxide (E_CO) and the binding energy of oxygen (E_O). Scaling relationships are found thr…
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This is an interesting article that describes a well-engineered, robust/reproducible, and very accessible (Jupyter notebooks) Poisson-Boltzmann solver. The authors have done an excellent job describin…
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I'm looking to perform some alchemical free energy calculations and recently started using OpenMM to do this. You've all done some nice work here, so I don't want to re-invent the wheel, but I initia…
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When I do not set boundary compositions for a specific model, the model runs fine, but after a while erroneous compositions flow in. When I set the boundary compositions to intitial compositions the f…
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There has been no activity since February, is the project still active? How can we move It forward?
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The authors present a python PB solver based on a fast multipole method library and a Galerkin boundary element method package. The method integrates a python interface with optimized computational ke…
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Hi everyone,
I just finished 2 sets of Gromacs simulation for my system (RNA+ligand). The first set has only ligand (20 runs). The second set has both RNA and ligand (30 runs). Each simulation is ru…
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Psi4 modules writing their variable to globals should be moved to Wavefunction local variables. This is part of the general "localization" of Psi4 to assist in complex Psi4 runs involving multiple com…