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Follow-up from #509 and #508
We would like to add support for doing AFE calculations using future releases of OpenFF force fields that will contain virtual sites.
This is a partial roadmap item …
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I have defined a CustomNonbondedForce to calculate the non-bonding force between LIPF6 and EMC, but the original non-bonding force in the system needs to be deleted. I use nbforce.addException(i,j,0.0…
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I was trying to run the Alchemical free energy calculations example as is on a CPU and a gpu - both cases don't run to completion.
but the errors are different.
On the cpu I get
Minimizing energy…
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We are currently working on obtaining free energy information for a large protein complex using a coarse-grained Martini model in OpenMM. However, we've encountered challenges in aligning our calculat…
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When we refactor the relative alchemical factory to move it to `openmmtools`, we should consider allowing multiple alchemical regions to enable A->B and B->A transformations to happen with the same si…
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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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Dear OpenMM community,
We (the Riniker lab @rinikerlab and the Hünenberger lab @csms-ethz at ETH Zurich) have developed a shifted reaction-field (RF) correction (https://doi.org/10.1039/D0CP03835K…
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This is intended for validation/accuracy assessment of alchemical free energy calculations; much less on "Can this method converge to the known correct answer for this given system and parameters?" (a…
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This is related to #3166 where I am trying to write a class that creates an alchemical hybrid system for running relative free energy calculations. The hybrid system will handle:
1) alchemical modif…
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**In broad terms, what are you trying to do?**
Run absolute binding free energies (ABFE) for host-guest or protein-ligand systems on a scale ranging from 100-1000 systems. This is for benchmark…