In the Federal government, almost all new hires (including most promotions) have a “probationary” period. IT HAS NOTHING TO DO WITH POOR PERFORMANCE! Anyone who says otherwise is lying.

Aside from the widespread personal misery that cutting probationary employees from the NIH is going to cause, it’s also going to set crucial research back by months or even years. Research/science and health are inextricably linked. Can someone please stop this!?

This week has been the longest year ever 😩

Over half of my tweets deleted now, from nine hundred something down to 450. It’s really a shame what the platform turned into. Some quality content has been lost forever.

So I don’t use that other site anymore and haven’t for a long time now, but I’ve finally started purging and deleting all my old tweets. Apparently that’s the best way since if you just delete your account someone can take your old handle.

GitHub - Lemkul-Lab/gamd_livecoms_tutorial Contribute to Lemkul-Lab/gamd_livecoms_tutorial development by creating an account on GitHub.

We have a new #tutorial posted online, this time for Gaussian-accelerated MD as implemented in NAMD. Article has been submitted to LiveCoMS, a great venue for such efforts. We welcome feedback! Yes, it's alanine dipeptide, but you have to start somewhere :) #compchem

github.com/Lemkul-Lab/g...

Read Martin Luther King Jr.'s 'I Have a Dream' speech in its entirety Americans across the U.S. are celebrating King's legacy this weekend. One way to reflect on his life and message is by revisiting his celebrated 1963 speech delivered at the Lincoln Memorial.

“This is no time to engage in the luxury of cooling off or to take the tranquilizing drug of gradualism.” MLK’s “I Have a Dream” speech is full of incredible prose and ideas, and is well worth a reread today: www.npr.org/2010/01/18/1...

This is a worrisome time to be a Fed. All that I and my coworkers in the govt. want to do is our jobs to the best of our ability. Hopefully we will be allowed to do that over the next 4 years. 🤞

Are @zbmed.bsky.social aware of the negative reaction on social media to their just-announced contract with MDPI. There's a great many red flags they seem to have missed, e.g.
deevybee.blogspot.com/2024/08/gues...
deevybee.blogspot.com/2024/02/the-...
+ @hansonmark@bsky.social's account below

A close up of an IgG1 Fc domain glycan (blue) and its attachment point (green)

An IgG1 antibody shown in secondary structure ribbon with coarse grained beads overlapping

Using SIRAH to coarse grain my glycosylayed antibody! Hooray for (1) tutorials that work, and (2) my first foray into CG! Can I join the #glycotime club?

Interviewer: Can you explain this gap in your resume?

Me: We lost 2 drives simultaneously in our RAID 1 array.

Tired of how slow hierarchical clustering is? Tired of finding optimum k values for k-means? We present eQual to you: biorxiv.org/content/10.1... the last member of the #MDANCE family, it bridges the gap between k-means and HAC. Thanks to @lexinc.bsky.social and @daniel-r-roe.bsky.social!

I do all my coding with vim. It’s everywhere and reliable though a terminal.

It was successful! 😌

No matter how experienced with computers I get, BIOS updates will always stress me out.

A great thread and an important read. All of the women scientists I know are extremely driven and talented, and often face barriers men simply don’t face. The scientific community as a whole will benefit if we can knock down these barriers and biases.

Calling all systems and computational biologists in search of a faculty position:

We have Assistant and Associate Professor positions! 🚀

Pittsburgh is beautiful, and we are doing amazing science here.

cfopitt.taleo.net/careersectio...

cfopitt.taleo.net/careersectio...

Please apply by Dec 2!

Forgot to mention it! “Über Schwingungen in Raumgittern” (‘On vibrations in space lattices’ according to google translate) by M. Born & Th. von Kármán.

The internet is amazing. I wanted to get the original (afaik) periodic boundary conditions paper, which was published in a long-defunct German journal in 1912. After some googling I found it in an archive at Princeton and am using google translate to read it. So awesome!

We are looking for a #CompChem postdoc to implement MELD (Modeling Employing Limited Data) into the AMBER suite of programs and test new applications in integrative modeling. Work with
@adrianroitberg.bsky.social
and me at #UFChemistry! Apply here explore.jobs.ufl.edu/en-us/job/53...

It feels like the barrier to starting a paper is so high, but once you get started it can be a lot of fun. It sparks lots of questions like “Oh yeah, why did I do that?” and “wait, why did I think this plot made sense?”

I’m surprised “cpptraj” isn’t bigger…

It depends on how critical sampling/convergence are to the question you are trying to answer. If it’s critical, any slowdown can be a pain.

I love stuff like this. MD is so much fun!

Hard to go wrong with souvlaki.

Well this doesn’t seem right…#imagingfail

Will there be a Combat tournament? Used to love that game 😀

modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields Modified nucleic acids have surged as a popular therapeutic route, emphasizing the importance of nucleic acid research in drug discovery and development. Beyond well-known RNA vaccines, antisense olig...

I do molecular dynamics simulations of biopharmaceutical molecules, both protein and nucleic acid (RNA 4ever). Here’s a link to a recent project, modXNA, which parameterizes any combo of base/sugar/bb nucleic acid modification for an MD sim: pubs.acs.org/doi/10.1021/...

Any misgivings I might have had were immediately dispelled when I logged on (after a year of inactivity) and found two reprehensible people that I never followed (you can guess who) figuring prominently in my notifications 😤