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PLUMED-NEST retweeted
📢 New #preprint describing our community effort to share #plumed tutorials arxiv.org/abs/2412.03595 ! Explore the tutorials at plumed-tutorials.org
PLUMED-NEST retweeted
Do you want to work at the interface of molecular simulations, structural biology experiments and #AI? Come to Paris for a PhD at @institutpasteur. 1 PhD position is available in our lab funded by @ERC_Research. Please repost!! #compchem #compbio Info 👇 research.pasteur.fr/b/15Hr
PLUMED-NEST retweeted
Support the statement!
Signed by over 120 experts, our letter highlighting the urgent need for a collaborative effort to establish a #FAIR database for #MolecularDynamics simulation data, is now on Arxiv.
📎 Read it here: bit.ly/3WjcC7x
📝Support our statement: bit.ly/3zVS3qm
#MDDB
PLUMED-NEST retweeted
Cool new feature in PLUMED-NEST. You can quickly find out all the @plumed_org input files that use specific actions, like METAD, and learn from real-life examples. Thanks Gareth Tribello! Try it out here: plumed-nest.org/browse.html
PLUMED-NEST retweeted
Alchemical flying gaussian method in @plumed_org plumed-nest.org/eggs/20/013/ @PlumedN sciencedirect.com/science/ar…
PLUMED-NEST retweeted
Tired of the usual online cooking classes? Check out the new PLUMED Masterclass: a series of virtual and interactive lectures on @zoom_us focused on basic and advanced topics in #moleculardynamics #compchem #OpenSource. Places are limited! Register now:
plumed.org/masterclass
Vintage PLUMED input files from the 2015 Parallel Bias Metadynamics paper by @BonomiMax and @JimPfaendtner now available on PLUMED-NEST
plumed-nest.org/eggs/20/020/
All the data needed to reproduce the simulations are available on PLUMED-NEST: plumed-nest.org/eggs/20/006/
A combined activation mechanism for the glucagon receptor #plumed pnas.org/content/early/2020/…
All the data needed to reproduce the cryo-EM-driven MD simulations are available on PLUMED-NEST
plumed-nest.org/eggs/20/015/
Very proud of this work led by @AvedaSci @eliasndaru and @alisa_garaeva with fantastic collaborators @CPaulino_ @BonomiMax, Dirk Slotboom, and Christof Grewer. We use modeling, cryo-EM, synthetic chemistry, and functional assays to characterize ASCT2
biorxiv.org/cgi/content/shor…
PLUMED-NEST retweeted
We just published a new paper on JCP with Roberto Car! We use the new #EnvironmentSimilarity CV in #PLUMED to study the phase equilibrium of ice and water. All input files available in #plumednest. Raising the bar for accurate free energies of solids! aip.scitation.org/doi/full/1…
All input files available here!
plumed-nest.org/eggs/20/010/
We just published a new paper on JCP with Roberto Car! We use the new #EnvironmentSimilarity CV in #PLUMED to study the phase equilibrium of ice and water. All input files available in #plumednest. Raising the bar for accurate free energies of solids! aip.scitation.org/doi/full/1…
PLUMED-NEST retweeted
Our new preprint on k_off calculation of a ligand inside a receptor using frequency-adaptive MetaD is out on @biorxiv_biophys !
And the input files are on #plumednest egg 20.005!
#compchem
biorxiv.org/content/10.1101/…
PLUMED-NEST retweeted
with source data available on #plumednest plumed-nest.org/eggs/19/076/
PLUMED-NEST retweeted
A good reason to remind us all of a common misconception of the folding funnel: The narrowing of the funnel towards the native state doesn't imply some sort of "guiding"; rather the opposite. This commentary by Martin Karplus is worth reading: doi.org/10.1038/nchembio.565
The Beautifully Orchestrated Symphony of Protein Folding within the Folding Funnel ow.ly/h1Zf50y2mMv
PLUMED-NEST retweeted
Something fun: We show that you can use enhanced sampling techniques to mimic a vibrational nonequilibrium and study its impact on chemical reactions.
pubs.acs.org/doi/10.1021/acs…
Only off-the-shelf software required + inputs are available through @PlumedN plumed-nest.org/eggs/19/080/
PLUMED-NEST retweeted
Our paper on the role of base-pair asymmetry in helicase unwinding dynamics has been published on @PNASNews! pnas.org/content/early/2019/…
PLUMED-NEST retweeted
Have you registered yet? Join tomorrow's #webinar on "Enhanced molecular simulations with PLUMED", 15:00 CEST with Gareth Tribello. @GTribello @plumedN @plumed_org
bioexcel.eu/webinar-enhanced…
PLUMED-NEST retweeted
Data and #plumed input files to reproduce the results of "Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways" (doi.org/10.1021/acs.jctc.8b0…) done with @CompBioPhys are now available in #plumednest plumed-nest.org/eggs/19/067/