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I think I am running out of memory even with 392GB for running standard pipeline for molecules size of ribociclib (62 atoms). The input for python poltype.py is:
```
structure=ribociclib.sdf
scrat…
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Hello,
I'm running ABFE calculations using a version of Sire modified to use Boresch protein-ligand restraints (https://github.com/fjclark/Sire/tree/feature_boresch_restraints). During the stage i…
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Dear OpenMM team,
I would like to run free energy simulation with protein-ligand interaction with your MD engine, but I could not find a proper tutorial or information related to that.
Could you…
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Now that we have BAOABLangevinIntegrator, we should think about updating our recommended simulation settings. These settings come up in lots of places:
- They're used in examples.
- They're recom…
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Hi there! I've been trying to run the "Alchemical Free Energy Calculations" Tutorial on the OpenMM Page. When I try to import openmmtools I get the following traceback:
---------------------------…
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I'm new to alchemlyb and python programming and want to analyze free energy calculations (Gromacs-based) using alchemlyb and I want to implement postprocessing to convert energy units to KJ/mol, with…
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#3286 added a number of helpful checks for valid parameter values, but it also appears to have [restricted `sigmaScale` and `epsilonScale` `NonbondedForce` parameter offset scaling factors to be nonne…
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I'm analyzing free energy calculations (Gromacs-based) using alchemlyb. The analysis fails due to the following error:
Traceback (most recent call last):
File "/home/home/miniconda3/lib/python3.8/…
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This is part of my crusade against API consumption of `Topology` :stuck_out_tongue:
Would it be crazy to refactor the parts of `from_smirnoff` that apply the force field out into an `parametrize_s…
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After downloading the benchmark tar file from
https://ambermd.org/GPUPerformance.php
If one wants to run the single core cpu cases, should one do
./runBenchmarks.sh -NGPU 0, -NCORE 0
Are th…