OpenMM: A high performance toolkit for molecular simulation https://xitter.cf/t.co/q9nYueNPsC
Joined May 2020
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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…
OpenMM retweeted
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
OpenMM retweeted
Nice benchmark data of OpenMM with GPU!
blog.salad.com/openmm-gpu-be…
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!
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!
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/…
OpenMM retweeted
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…
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
OpenMM retweeted
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)
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
OpenMM retweeted
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?
OpenMM retweeted
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!
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…
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/…
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.
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
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….
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…