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Hello,
The implementation of OpenABC is very useful, I have been able to create and simulated a condensate slab in the course grained environment provided by OpenABC-openmm. The issue I am running i…
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For the new user, the first question when using the GUI would be--what are we optimizing when selecting "optimization"? For us, it is obvious that cost optimization, and thus minimization of the LCOW,…
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I set up a toy system primarily consisting of water, with alanine-dipeptide placed in the corner.
During a custom energy minimization (essentially gradient descent using the forces from `getForces…
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hello there, I have been trying to find a way to have a periodic boundary where cells would be limited to a box and I finally got to this notebook : PeriodicBoundaryConditions.ipynb
where it uses s…
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**Describe the solution you'd like**
need to show the energy of a molecule from optimization. I use this in teaching undergraduate chemistry students organic molecule energy minimization. Used to c…
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**Is your feature request related to a problem? Please describe.**
I ran a LAMMPS/CGDNA simulation (oxDNA2) and considered comparing the energies computed by the simulation for a selected structure w…
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The OneShiftOnly optimizer minimizes only the total energy and is not capable of variance minimization, or minimization of mixtures of energy and variance.
Additionally, the default cost function (…
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Energy minimization should clean-up many of the high energy structures generated with the build command. Build in a separate energy minimization module or add a flag to build command?
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## Description
The OpenBabel documentation names two different default values for the `-ff` parameter in two different places:
This section says the default is `Ghemical` in two places:
[forcef…
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I'm trying to run energy minimization of a protein-ligand complex (topology defined by `top`, protein atom indices defined by `protein)` and extract the interaction energy afterwards, based on the sni…