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Simulations can crash (give NaN errors) if the protein has not been equilibrated first. Maybe we could add a warning or note in the documentation that proteins may need to be equilibrated (short minim…
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The protein-small molecule complex generated by RFAA has numerous clashes, and even after energy minimization with Schrodinger, there are still many clashes. Does this mean that the resulting structur…
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It would be useful to check the NetCDF file for whether minimization and energy computation need to be performed during `run` operations, rather than requiring these be done during `setup` since they …
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I am running some psi4 jobs which involve modifying the parameters DFT_VV10_B and DFT_VV10_C for various benzene dimer configurations. For several dimer configurations and several values of (b,c), I g…
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Could you also merge the updates to scoring functions and high-performance energy minimization etc from https://github.com/mwojcikowski/smina
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Hello,
The Galaxy module "Extract energy components with GROMACS" is supposed to take EDR files as input (e.g. from modules like GROMACS energy minimization or GROMACS simulation) but does not allo…
vinbl updated
4 years ago
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I'm investigating a problem reported by a user who is using PLUMED with OpenMM: https://github.com/openmm/openmm-plumed/issues/65. They report that it creates an empty COLVARS file, while writing the…
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Hello, everyone!
I'm working with two molecules, 6LFR and 7LFR, provided to me in the `*.mol` format. They consist of 236 and 275 atoms, respectively.
To check the consistency of the results obt…
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**Is your feature request related to a problem? Please describe.**
Open Babel is not able to assign correct atom types (eg. for force field usage) of ionized molecules. This is typical for molecules …
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Hello! I'm new to OpenMM and would like to use it to estimate vibrational frequencies and normal modes of molecules.
My understanding is that this could be done by doing an energy minimization step…