@daniel-r-roe.bsky.social
Computational chemist, scientific software developer (Amber/CHARMM), author of CPPTRAJ.
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.
February 21, 2025 at 1:30 PM
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!?
February 14, 2025 at 7:11 PM
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 😩
January 30, 2025 at 1:30 AM
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.
January 22, 2025 at 9:08 PM
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.
January 22, 2025 at 8:01 PM
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.
Reposted
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...
github.com/Lemkul-Lab/g...
GitHub - Lemkul-Lab/gamd_livecoms_tutorial
Contribute to Lemkul-Lab/gamd_livecoms_tutorial development by creating an account on GitHub.
github.com
January 21, 2025 at 7:21 PM
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...
github.com/Lemkul-Lab/g...
“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...
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.
www.npr.org
January 20, 2025 at 9:04 PM
“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. 🤞
January 20, 2025 at 8:55 PM
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. 🤞
Reposted
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
deevybee.blogspot.com/2024/08/gues...
deevybee.blogspot.com/2024/02/the-...
+ @hansonmark@bsky.social's account below
December 21, 2024 at 1:20 PM
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
deevybee.blogspot.com/2024/08/gues...
deevybee.blogspot.com/2024/02/the-...
+ @hansonmark@bsky.social's account below
Reposted
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?
December 3, 2024 at 9:00 PM
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?
Reposted
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!
biorxiv.org
December 5, 2024 at 6:09 PM
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!
No matter how experienced with computers I get, BIOS updates will always stress me out.
December 3, 2024 at 2:05 PM
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.
Women are under-represented at senior levels in #academia globally, & across all #science 🧪 disciplines, as shown by these "scissor-shaped curves" ✂️
So how can we ever achieve #gender #equality?
We discuss various strategies in this #Cell Commentary
#WomeninSTEM
www.cell.com/cell/fulltex...
🧵 1/
So how can we ever achieve #gender #equality?
We discuss various strategies in this #Cell Commentary
#WomeninSTEM
www.cell.com/cell/fulltex...
🧵 1/
December 1, 2024 at 12:37 PM
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.
Reposted
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!
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!
Faculty.Professor.Assistant - Full-Time
Click the link provided to see the complete job description.
cfopitt.taleo.net
November 20, 2024 at 1:58 PM
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!
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!
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!
November 30, 2024 at 2:38 PM
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!
Reposted
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...
@adrianroitberg.bsky.social
and me at #UFChemistry! Apply here explore.jobs.ufl.edu/en-us/job/53...
University of Florida - Details - Post-Doctoral Associate in Computational Chemistry
explore.jobs.ufl.edu
November 26, 2024 at 3:48 PM
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...
@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?”
November 27, 2024 at 1:23 AM
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?”
Hard to go wrong with souvlaki.
November 19, 2024 at 10:57 PM
Hard to go wrong with souvlaki.
Well this doesn’t seem right…#imagingfail
November 16, 2024 at 10:42 PM
Well this doesn’t seem right…#imagingfail
Reposted
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/...
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...
pubs.acs.org
November 15, 2024 at 1:44 PM
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/...
Just made my final post on that _other_ site, downloaded my archived data, and am getting ready to delete the account. Not much but it’s something.
November 15, 2024 at 2:07 PM
Just made my final post on that _other_ site, downloaded my archived data, and am getting ready to delete the account. Not much but it’s something.
It’s that time of year again when all the hip new cold viruses are going around and your kids make sure that you are among the first to experience them 😩
November 14, 2024 at 7:02 PM
It’s that time of year again when all the hip new cold viruses are going around and your kids make sure that you are among the first to experience them 😩
The Bluesky “starter pack” concept is a really awesome idea!
November 13, 2024 at 10:09 PM
The Bluesky “starter pack” concept is a really awesome idea!
For anyone else hitting the “Invalid handle” issue, this helped me solve it!
One part of our upgraded infrastructure may affect your profile.
If you see your handle now says “Invalid handle,” please reverify it by navigating to Settings > Change my handle > Type in your current handle > Verify DNS Record > Update.
(Basically, update to the same handle.)
If you see your handle now says “Invalid handle,” please reverify it by navigating to Settings > Change my handle > Type in your current handle > Verify DNS Record > Update.
(Basically, update to the same handle.)
November 13, 2024 at 2:05 AM
For anyone else hitting the “Invalid handle” issue, this helped me solve it!