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Hello. You have recently added the ensemble TI spring to the GPUMD software, allowing the users to calculate the absolute free energy of a crystal via the Frenkel–Ladd path.
I am writing to ask if …
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Hi,
I have already executed simulations for my membrane protein complexes, I have over 30 complexes. I have executed relative binding affinities and now want to execute absolute binding free energy c…
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Currently we only support relative free energy calculations but absolute solvation free energy calculations are routinely carried out in the field with well described protocols.
@lohedges @ppxasjs…
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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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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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Currently, at least for somd, it appears it isn't possible to setup input files for a free energy calculation in one BioSimSpace script, and load the input and run a free energy calculation with a sep…
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Hi,
To mitigate the statistical errors inherent in QCG calculations, it's suggested to conduct solvation free energy computations several times and then average the outcomes to minimize uncertainty. …
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Trying to enumerate all the ways that perses can be used, and might be used in future
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I'm running through the code and am a bit confused on some of the code choices. For example, For example, B1 and B2 solvent files have different lambda restraints.
bond_energy_function = "lambda_re…
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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…