OpenMM: A high performance toolkit for molecular simulation openmm.org
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The OpenMM 8.2 release candidate is out!
You can install it with:
mamba install -c conda-forge/label/openmm_rc -c conda-forge openmm
Please test to make sure that everything works for your applications:
simtk.org/plugins/phpBB/view…
OpenMM 8.2 release notes:
simtk.org/plugins/phpBB/view…
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We are excited to share the update that our project OpenMMDL has been accepted as MDAKit, now available at MDAnalysis mdanalysis.org/ and via conda forge github.com/wolberlab/OpenMMD…
@openmm_toolkit
@VTalagayev
@YuChen_istry
@Habacef
@jchodera
@orbeckst
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OpenMM retweeted
We're hiring an OpenMM software scientist to join our team to work on community driven software projects! The position is hybrid- and remote-eligible.
careersearch.stanford.edu/jo…
Please RT and help spread the word!
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OpenMM retweeted
New blog post - how to run MD simulations of organic molecules using OpenMM. This seems simple, but I've tried and failed to figure out how to do this a decent number of times over the past five years!
corinwagen.github.io/public/…
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Unbiased dynamics from biased MD simulations: the implementation of Girsanov reweighting in OpenMM via openmmtools for on-the-fly calculation of reweighting factors and the implementation in Deeptime for reweighted Markov state models. @BettinaGKeller
pubs.acs.org/doi/full/10.102…
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OpenMM retweeted
🚨🚨🚨NEW SOFTWARE RELEASE!🚨🚨🚨
Help advance biomedical research by downloading/installing our new client software from
foldingathome.org/start-fold…
This release has an improved UI and the option to control all the machines you have running Folding@home from a single webpage
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We've implemented all algorithms in the Python package A3FE (Automated Adaptive Absolute alchemical Free Energy calculator, github.com/michellab/a3fe), which is based on BioSimSpace and Sire from OpenBioSim, and uses OpenMM for MD. (5/6)
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OpenMM is thrilled to be funded through @cziscience EOSS6 via @wellcometrust to support a community-oriented developer position to better meet the rapidly growing needs of the biomolecular simulation community! 🎉
Open source tools are crucial for biomedical research. We're collaborating with @KavliFoundation + @Wellcometrust to support developers & maintainers of critical #OpenSource projects, promoting innovation & community engagement in the field. More ▶️ czi.co/3zjN56l
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another interesting simulation series by rotation student Ashley Lasko using @openmm_toolkit - in this case asking what happens differently if just one telomere is anchored on the nuclear envelope, instead of both of them?
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Biophysics grad program flash talk today from rotation student Ashley Lasko, jointly mentored with @WallaceUcsf , showing her work modeling meiotic chromosome motion and pairing using
@openmm_toolkit Great work Ashley!
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In case you missed it, the SPICE 2.0 quantum chemical dataset is here!
We're excited to announce SPICE 2.0, a new foundation QM dataset for building ML potentials for biomolecular simulation! 🚀
💊 13K new PubChem molecules
🌊 water clusters and solvated molecules
🤝 amino acid-ligand pairs
⚛️ more elements (B, Si)
github.com/openmm/spice-data…
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OpenMM retweeted
Happy to hear that there is an option from @openmsf! And also Schrodinger supporting academic licensing (finally!). We find @openmm_toolkit very useful because of its unparalleled flexibility. Their work is an incredible force in this field.
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OpenMM retweeted
GB99dms is an enhanced force field optimized for disordered proteins using differential molecular simulations. It improves structural accuracy and is now available for OpenMM. #moleculardynamics
biorxiv.org/content/10.1101/…
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OpenMM retweeted
Spotlight on our next two notebooks: Introducing MARTINI force field MD simulations for proteins with OpenMM engine (Hats off to @SouzaPauloCT, @jlmaccal, Valentina Corradi, D. Peter Tieleman). Oh, and you can convert those coarse trajectories with cg2all to atomistic.
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OpenMM retweeted
Explore the world of molecular mechanics with #OpenMM, a high-performance open-source toolkit for simulating biomolecular systems.
openmm.org
#MolecularMechanics #Simulations #MD #CompChem
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OpenMM retweeted
Using the power of @ambermdprog, @openmm_toolkit, @openforcefield, @CG_Martini, and the ever-powerful @GoogleColab, we've crafted 3 sparkling new cloud-computing workflows for MD simulations. Dive in right here: github.com/pablo-arantes/mak….
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We're excited to announce SPICE 2.0, a new foundation QM dataset for building ML potentials for biomolecular simulation! 🚀
💊 13K new PubChem molecules
🌊 water clusters and solvated molecules
🤝 amino acid-ligand pairs
⚛️ more elements (B, Si)
github.com/openmm/spice-data…
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