Author Archives: Will Kennerly

Justin and Kristine present research at national American Chemical Society meeting in San Francisco

On April 3, 2017, senior chemistry majors Justin Gerard and Kristine Vorwerk traveled to the national American Chemical Society meeting in San Francisco to present their research.   They each presented a poster.  Kristine presented on her progress using the software package Newton-X developed by the Barbatti group to calculate absorption spectra of indole, as well as calculate surface-hopping trajectories of excited-state indole.  Justin presented his conclusions about appropriate functionals to use for TD-DFT absorption and fluorescence calculations, both in the gas phase and with a state-specific solvation method.  Great work Kristine and Justin!


Justin Gerard proudly stands by his research poster at the Spring 2017 national ACS meeting in San Francisco.




Kristine Vorwerk gesticulates about science while presenting her poster at the Spring 2017 national ACS meeting in San Francisco.


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Research Group, Spring 2017

The Spring 2017 semester has started, and as appropriate for the coming season, the group has sprouted in size — eight student members!


Kennerly Research Group, Spring 2017. From (left to right):  Will Magee ’19, Justin Tam ’19, Ryan Dohrn ’20, Annabel Pruitt ’20, Ethan Celebuski ’19, Kristine Vorwerk ’17, Justin Gerard ’17 and James McKee ’18

Will, Annabel and James will be working on developing our molecular dynamics simulations and analyses of Trp-containing proteins.  Justin T, Justin G, and Kristine will be working on various aspects of the quantum mechanics/dynamics of indole using Gaussian and NewtonX.   Ethan will be developing an instructional exposition on analyzing hybridization using Gaussian.   Ryan will be python scripting to support our never-ending needs for parsing and analysis.

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Kristine and Justin present research at Chemistry Department Winter Celebration

A bit belated recognition here, but in December at the end of the fall semester, Justin Gerard ’17 and Kristine Vorwerk ’17 each presented a poster at Skidmore College’s joint Chemistry/Biology winter celebration.  Justin presented on his continued efforts to analyze functionals and basis sets for their suitability for calculating indole’s vertical absorption and emission energies, which turns out to be quite tricky business.   Kristine presented on her new focus on using a free research-grade software package called NewtonX to calculate indole’s absorption spectra with more structure than a traditional software like Gaussian typically produces.  Good work this semester!

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MERCURY conference 2016 — a great time for students to experience computational chemistry!

Alexandra Cassell presenting her poster at MERCURY 2016

Alexandra Cassell presenting her poster at MERCURY 2016

Last week  Alex, Justin and I traveled (along with the Navea group) to the MERCURY conference at Bucknell University,
a conference devoted to computational chemistry done by undergraduates.  Its a a great opportunity to see the wide diversity of work that qualifies as ‘computational chemistry’, everything from really detailed studies of small molecules using high-level theory, to simulations of huge biomolecules with an aim towards discovering better drugs.   Not to mention mechanistic organic chemistry, applied materials research, and lots more.     Six speakers from research institutions and companies also come in to talk about their careers and research programs.   Its a not-to-miss conference every year!

Justin Gerard presenting his poster at MERCURY 2016

Justin Gerard presenting his poster at MERCURY 2016

Justin and Alex both presented results from their summer research on excited-state time-dependensity density functional theory calculations of indole and tryptophan (respectively).  Both spoke for a quick 1-minute abstract talk in front of the entire audience of 100+ attendees and then presented their poster for an hour during the poster session, speaking with other students, faculty at undergraduate colleges, and the six invited speakers.    Justin and Alex have posted trip reports.    Here are the vital pictures  — they both did a great job!


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Charles presents at Skidmore Student/Faculty summer research meeting; thanks Charles!

Today a bunch of summer research students presented the results of their 5 weeks of work (for the first-half of the summer term).  Charles (math major, class of 2018) started off this summer working in our group; he has never taken a chemistry class and in just five weeks managed to learn how to run molecular dynamics simulations with AMBER (and updated and corrected some of our tutorials) and wrote some python and cpptraj scripts to aid in our analysis of melittin trajectories.  Charles has now had enough of pretending to be a chemist and is going back home for the summer.   The group will be building on your work next semester.  Thanks Charles!



Charles Clayton and his poster — “Structural Changes of Tryptophan in a Melittin Molecular Dynamics Simulation”


Not many people have the guts to present a science poster wearing a baseball cap. At least it wasn't the Red Sox.

Action shot — Charles handles the crowd around his poster!

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Writing scripts to submit jobs on comet using the slurm queue manager

Comet is a huge cluster of thousands of computing nodes, and the queue manager software called “slurm” is what handles all the requests, directs each job to a specific node(s), and then lets you know when its done. In a prior post I showed the basic slurm commands to submit a job and check the queue.

You also need to write a special linux bash script that contains a bunch of slurm configurations, and also the linux commands to actually run your calculation.  This is easiest show by example, and I’ll show two:  one for a Gaussian job, and another for an AMBER job.

#SBATCH -t 10:00:00
#SBATCH --job-name="gaussian"
#SBATCH --output="gaussian.%j.%N.out"
#SBATCH --partition=batch
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --export=ALL

jobfile=YOURINPUTFILE  #assumes you use a gjf extension (which is added below)

. /etc/profile.d/
module load gaussian
exe=`which g09`
export OMP_NUM_THREADS=$nprocshared
/usr/bin/time $exe < $jobfile > $outputfile

If you copy this file exactly and then modify just the important parts, you can submit your own Gaussian jobs quickly.   But its worth knowing what these commands do.  All the SBATCH commands are slurm settings.  Most important is the line with the “t” flag which sets the wall time you think the job will require.  (“Wall time” means the same thing as “real time”, as if you were watching the clock on your wall.)  If your job winds up going longer than your set wall time, then slurm will automatically cancel your job even if it didn’t finish—so don’t underestimate.   The other important slurm flags are for “nodes” and “n-tasks-per-node”, which set how many nodes you want the job to use, and how many processors (cores) per node you want your job to use, respectively.  For Gaussian jobs, you always want to use nodes=1.  You can start with tasks-per-node=1, and then try and increase it up to 12 (the max for comet) to see if your calculation can take advantage of any of Gaussian’s parallel processing algorithms.  (You would also need to add a %nprocshared=8 line to the .gjf file.  It doesn’t always work that well, meaning your simply wasting processing time that we have to pay for.)

The commands at the bottom are bash linux commands that set up some important variables, including the stem of the filename for your Gaussian job file.  Eventually the script then loads the Gaussian module, and with the last line, submits your job.

If you’re using AMBER for molecular dynamics simulations, here’s a simple slurm script you can copy:

#!/bin/bash -l
#SBATCH -t 01:10:00
#SBATCH --job-name="amber"
#SBATCH --output="oamber.%j"
#SBATCH --error="eamber.%j"
#SBATCH --partition="compute"
#SBATCH --nnodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --no-requeue
#SBATCH --mail-type=END

module load amber

ibrun sander.MPI -np 1 -O -i -p -c 2mlt_equil3.crd -r 2mlt_equil4.crd -ref 2mlt_equil3.crd -x 2mlt_equil4.trj -o mdout

The SBATCH commands do the same job of configuring slurm, though the “mail-type” and “mail-user” options show how you can have slurm email you when a job finishes. In this example, the last ibrun command is the one that actually runs AMBER (a sander job) and sets up all of its settings, input files, output files, and other necessities. Those must be changed for each new job.

Here is some specific information and examples for comet at the San Diego Supercomputer Center, as well as a complete list of all the slurm options you can use.

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What you need to learn to do Computational Chemistry: everything Chris Cramer knows!

Doing computational chemistry requires (1) the technical know-how to use special software and computers and (2) the knowledge to understand what the software is telling you.

On that second point, there’s a lot of math and physics behind the theories of chemistry—and its great stuff! But before you dive into studying a lot of formal math and physics, its good to know what you’re working towards. Chris Cramer (a professor at U. Minnesota) is a computational chemist who has written a computational chemistry textbook and put a bunch of free video lectures up on Youtube that explain the concepts behind computational chemistry at a level that most students can understand. If you’ve taken general chemistry, an organic chemistry course, and a couple semester of calculus (multivariable calculus is great, but not absolutely necessary), these videos are great background and inspiration.  As you move through the video series (49 total — a full course!) the material gets rich, but if you follow along you should understand the spirit of it.

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Running a job on Comet – using the queue manager called SLURM

You tell comet to run your calculation by submitting it to a queue. Your calculation waits in line with all the other jobs scientists want to run on comet. The software that controls this queue is called slurm (that’s a really dumb name, but so it is).

The basics are that first you make (or edit) a bash script containing all the slurm settings and Linux commands you need.  Let’s say you call that file Then you can submit your job to the queue by typing:This ain't no cartoon


If it works, you should see a short message with the job’s ID number.   Your job might not start right away if there are a lot of either jobs ahead of yours in line.

To view all the jobs in the queue, you can just type


To view only the jobs you’ve submitted, you can just type

squeue -u yourusername

If you realize — whoops! — you made a mistake and want to cancel the job you’ve just submitted, you can type

scancel JobIDNumber

When your job is done, it will silently disappear from the queue and your output files should be in your directory.  You can put a setting in your script to email you when your job finishes.  If something went wrong with the calculation, your output files should contain error messages to help you figure out what went wrong so you can fix it and resubmit the job.

That’s it for the basics.  There are some more useful slurm commands you can read about on the slurm official documentation page.  In another blog post, I’ll show you a simple slurm script you can copy, paste, and edit to get your own jobs running smoothly.

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Accessing Comet at SDSC

Don't let it hit youComet is the supercomputing cluster at the San Diego Supercomputing Center that we have been using to help us do calculations.  We have access to comet with support from XSEDE (thank you!)

Comet is accessed over the internet using a command-line interface on the server  The basic program we use to access comet is called “ssh” (which is an acronym for “secure shell”).

On Mac OSX, you can go to Applications -> Utilities -> Terminal to open the command-line Linux interface on your mac.   To login to comet from your mac, in the Terminal program type: ssh Of course, use your own comet username in place of mine!

On Windows, there is no command-line Linux interface, so you need to use a separate program to connect to comet using ssh.  The classic program is called putty, and it is pre-installed on all Skidmore-owned Windows computers.  You may prefer to get a program with more features, for example, the Bitvise ssh client .  In either case, download and install a ssh program and tell it to access

On either type of computer, after a few seconds, you will connect to comet and be prompted for your password.  After you type in your password, you will be looking at a Linux command line (specifically, it is a bash prompt) on a computer 3000 miles away from Saratoga Springs.  Cool, eh?

Now you can use comet for whatever calculation you need, using Linux commands, your input and output files (for gaussian or AMBER)

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Accessing Skidmore’s datastor server and our KennerlyResearch shared folder

Our research group has a special folder on the Skidmore server “datastor” where we all keep things we’re working on and sharing.

On Mac, connect to the server smb://

On Windows, connect to //

If you’re on a Skidmore computer, there is likely a “Datastor” icon on your desktop that will connect you automatically.

After you connect to datastor, look for the “Netshare” directory and then the subdirectory “KennerlyResearch”.


If this is your first time doing this, you can follow these instructions at the link below for more details.  Also, you will need to ask me to add your Skidmore username for permission to read and write files in KennerlyResearch.

On Windows:

On Mac:

If you are on-campus, it is quick and easy to get access to the folder.

If you are off-campus, you will need to install VPN software called “Cisco AnyConnect” to securely connect back to Skidmore’s intranet.  The links above have instructions for doing that for both Windows and Mac.

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