Our team @snbkol introduces PathGennie (just published in @JCIM_JCTC), a fast and unbiased computational framework for uncovering rare molecular events such as drug unbinding and protein folding. Instead of using any biased forces or elevated temperatures, PathGennie launches ultrashort unbiased MD trajectories and selectively propagates only those that show real progress toward the transition. This lets us generate complete rare-event pathways in just 10–100 ps, while preserving true molecular dynamics. Full credit goes to my PhD student Dibyendu Maity @MAITYDIBYENDU99 for formulating and implementing the PathGennie code. Thanks to @ANRFIndia for funding. ✨ Key Highlights: • Identified 7 distinct unbinding routes for benzene from T4 lysozyme • Recovered all major exit pathways for imatinib from Abl kinase within a handful of attempts • Captured folding/unfolding pathways of Trp-cage and Protein G that align with minimum free-energy paths • Weighted Ensemble (WE) simulations converge 3–4× faster when initialised with PathGennie-generated pathways • Path finding works even with suboptimal CVs 🔗 Try our code: github.com/TeamSuman/PathGen… 📄 Read the paper: pubs.acs.org/doi/10.1021/acs… #CompChem #RareEvent #EnhancedSampling #MolecularDynamics #PathSampling #DrugDiscovery

A beautiful baby crystal being born, or not? #NucleationRocks #ScienceArt #PathSampling #MolSim

4th first authored research article from my PhD work just got published in JCP (@AIP_Publishing) where we estimated the nucleation rate for CO2 hydrate formation using path sampling. aip.scitation.org/doi/pdf/10… #PhD #Science #Simulation #MD @pathsampling @UvA_Amsterdam @HimsUva

The @pathsampling wrapper wouldn't have been possible without the python module implemented by the @plumed_org team. Thanks a lot!

Happy to contribute to this powerful framework!

Haha , yep you co-authored them :D (pubs.acs.org/doi/10.1021/acs…). And indeed it has a nice twitter page & an active github maintained by @davidswenson :)

Those OPS papers look familiar 👀 But I didn't know they had a Twitter impersonation

as a side note- all type of path sampling (which is also enhanced sampling and Replica exchange) can be done one GPUs with @pathsampling . Super fast and useful

Also, there will be tutorials! Learn how to simulate protein-protein binding pathways as in pubs.rsc.org/en/content/arti…… using @WestpaSoftware and the state-of-the-art using @pathsampling, tauRAMD, @biosimspace, LOOS.

I supervised a thesis where Ids simulated opening & closing of T4 Lysozyme. In just 3 months we were able to generate 200 successful transitions. It's amazing to see the power of Transition path sampling written beautifully by @davidswenson in the package @pathsampling

How DNA bases "roll over": Using path sampling to study the mechanism and kinetics of transient Hoogsteen base pair formation in DNA. New publication is out: academic.oup.com/nar/article… @pathsampling

#PathSampling growing stronger!!

Omg! I am flattered. Still have 1 year left with Bolhuis lab but surely would love to sample barriers together. Will get back :)

😂😂 good luck. Wanna come here for a postdoc? We can overcome barriers together with flux :)!

New paper on the nucleation mechanism of hydrates from @wadhawanarjun and P. Bolhuis using the #spring_shooting and @pathsampling which identify transition states and enhance path sampling efficiency. Congrats!!

No. My official name on passport is only 'Arjun'. I am like Bond! ;)

Paper Out! I used @pathsampling to study #nucleation of Methane Hydrates. Thanks to Peter Bolhuis for hiring & inspiring me. #PhD pnas.org/content/early/2019/…

Concentration 🧠 at the coding session of the #ECAM2020 Extended Software Development Workshop in Topics in Classical MD @ENSdeLyon @pathsampling @cecamEvents cecam.org/workshop1802/

There is no going back from 'plum-ed'

Here’s the official pronunciation chirb.it/krGg8n