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Jan Jensen
Works at University of Copenhagen
Attended Iowa State University
Lives in Copenhagen
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Jan Jensen

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Finding disordered residues in an NMR ensemble
Note to self: here's how you identified disordered residues in the NMR ensemble 2KCU.pdb 1. In Pymol: "fetch 2kcu" 2. Action > align > states (*/CA) 3. "save 2kcu_aligned.pdb, state=0" 4. In terminal: grep CA 2kcu_aligned.pdb > lis 5. python disorder.py dis...
Note to self: here's how you identified disordered residues in the NMR ensemble 2KCU.pdb 1. In Pymol: "fetch 2kcu" 2. Action > align > states (*/CA) 3. "save 2kcu_aligned.pdb, state=0" 4. In terminal: grep CA 2kcu_aligned.pdb > lis 5. python disorder.py disorder.py (given below) calculates the ...
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Automating calculations: pKa predictions
I want to compute the standard free energy difference for proton exchange between heliotridane and a molecule which I'll call compound 1 (comp1) heliotridaneH+ + comp1 <=> heliotridane + comp1H+ To do this I need to geometry optimize in the gas phase and th...
To do this I need to geometry optimize in the gas phase and then do a single point calculation using a solvation model, all using GAMESS. I want to automate this so I can do it for comp2, comp3, ... To do this I use bash and the python programs listed below.
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2nd Reviews for Prediction of pKa values using the PM6 semiempirical method
The 2nd round of reviews on our latest PeerJ submission came in on July 7th.   The first round of round of reviews and a link to our response can be found here . Editor's Comments MINOR REVISIONS Thank you for your efforts at addressing the reviewer's comme...
Thank you for your efforts at addressing the reviewer's comments. In spite of that, the reviewers (and myself) still think that additional data should be moved from the Supporting Information to the main text as tables/graphs. Specifically: -per reviewer 1's request, please include the ref.
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Computational Chemistry Highlight: June issue
The June issue of  Computational Chemistry Highlights  is out. CCH is an  overlay journal  that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is ...
The June issue of Computational Chemistry Highlights is out. CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for ...
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Planned papers for 2016 - six months in
Pedro's post reminded me that mine was due In January I wrote about the papers I plan to publish and made this list: Submitted None Probable 1. Benchmarking of PM6 and DFTB3 for barrier heights computed using enzyme active site models. 2. pKa prediction usi...
Submitted None Probable 1. Benchmarking of PM6 and DFTB3 for barrier heights computed using enzyme active site models. 2. pKa prediction using PM6 - part 1 3. Protein structure refinement using ProCS15 - starting from x-ray structure. Maybe 4. PM6 for all elements in GAMESS, including PCM ...
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Different approaches to creating (meta-GGA) DFT functionals
Contributed by  David Bowler Reposted from  Atomistic Computer Simulations  with permission Within the DFT community, John Perdew’s idea of the Jacob’s ladder of accuracy [1]  starts with LDA, moves to GGAs with the inclusion of the gradient of the electron...
Within the DFT community, John Perdew's idea of the Jacob's ladder of accuracy[1] starts with LDA, moves to GGAs with the inclusion of the gradient of the electron density, and is further extended (to rungs three and four in the ladder analogy) with meta-GGA, where kinetic energy density is ...
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Jan Jensen

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slides for 2016 Gordon Research Conference in Computational Chemistry
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Reproducing stats or verbose output from LINEST command in Excel or Google Sheet
The code above reproduces the output produced by the LINEST(y;x;true;true) command in Excel [ LINEST(y,x,true,true) in Google Sheets] with a csv file as input.  In the csv file I have assumed that the x and y columns are labelled "x" and "y" respectively.  ...
The code above reproduces the output produced by the LINEST(y;x;true;true) command in Excel [LINEST(y,x,true,true) in Google Sheets] with a csv file as input. In the csv file I have assumed that the x and y columns are labelled "x" and "y" respectively. This page has a good explanation of the ...
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Computational Chemistry Highlight: June issue
The June issue of  Computational Chemistry Highlights  is out. CCH is an  overlay journal  that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is ...
The June issue of Computational Chemistry Highlights is out. CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for ...
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Systematic Error Estimation for Chemical Reaction Energies
Gregor N. Simm and Markus Reiher (2016) Contributed by Jan Jensen Simm and Reiher present an approach to estimate the error of density functionals parameterized for a specific system.  System-specific parameterization can yield very accurate predictions for...
Simm and Reiher present an approach to estimate the error of density functionals parameterized for a specific system. System-specific parameterization can yield very accurate predictions for the training set but the applicability of the resulting functional to any other systems, ...
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Reviews for Prediction of pKa values using the PM6 semiempirical method
Reviews of our latest PeerJ submission is in after only 15 days.  This must be some kind of record! Personal comments from the editor: Table 4 shows dramatic differences between PM6-D3H+ and PM6 although the previous tables did not show very large differenc...
Reviews of our latest PeerJ submission is in after only 15 days. This must be some kind of record! Personal comments from the editor: Table 4 shows dramatic differences between PM6-D3H+ and PM6 although the previous tables did not show very large differences between both semiempirical methods.
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Computational Chemistry Highlight: May issue
The May issue of  Computational Chemistry Highlights  is out. CCH is an  overlay journal  that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a...
The May issue of Computational Chemistry Highlights is out. CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for ...
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Have him in circles
960 people
Evgeni Zaytsev's profile photo
Muthu Vel's profile photo
Khem Adhikari's profile photo
Koen De Paus's profile photo
HDドラえもん's profile photo
H. Friederich's profile photo
Fuwei Zhuge's profile photo
Surinder Hundal's profile photo
Chris Genly's profile photo
Work
Employment
  • University of Copenhagen
    Professor of Bio-Computational Chemistry, present
  • University of Iowa
    1997 - 2006
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Copenhagen
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Introduction
I am a computational chemist working at the University of Copenhagen.  I work on protein design, quantum chemistry methods, and visualization
Education
  • Iowa State University
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Male