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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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This is a thread to discuss the creation of a tutorial showing how to implement free-energy perturbation using a network, e.g. generated by LOMAP, within BioSimSpace.
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I wanted to know if it is possible to use PyMBAR to generate a 2D Potential of Mean Force (PMF) graph using energies obtained from NAMD. The energies need to be reweighted though as I used accelerated…
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### Contact email
smostaj1@asu.edu
### ASURITE
smostaj1
### Cluster
Sol
### Software Name
Tinker-HP GPU
### Software version
current
### Link
https://tinker-hp.org
### Dependencies
NVHPC
…
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**In broad terms, what are you trying to do?**
[BindingDB](http://bindingdb.org) has a very large number (>1M) of binding free affinity measurements that we can use as a source of automating the cura…
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This Issue is intended to keep track of the examples that we could implement in the future. Please vote on these using 👍 if they would be useful to you.
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Hey,
as discussed in https://groups.google.com/forum/?utm_source=digest&utm_medium=email#!topic/hyperspy-users/7Z9DybWoU6s it would be nice to have a way to fit EELSCLEdge components to the continuum…
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Do OpenMM's PME implementations permit the dielectric constant at the boundary to be exposed as a user-settable parameter? I believe "tinfoil boundary conditions" are used right now, but it may be us…
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I've been running hamiltonian repex (for relative free energy calculations) using openmmtools. In the openmmtools implementation, we first propagate all replicas (run MD) and then compute the energy o…
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The authors stated that ``The sphere has a radius of 1 Å, and 100 charges are placed randomly inside, representing the atoms in the solute.'' This is unphysical. There cannot be 100 atoms in a sphere …