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Merge pull request #2 from langner/master

Some changes I made today.
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commit 1c9e0914e1e5a7e6f302ea24df18e0da82136e48 2 parents 6a7d3d0 + f29fe87
Karol M. Langner langner authored
Showing with 37 additions and 27 deletions.
  1. +11 −0 paper.bib
  2. BIN  paper.pdf
  3. +26 −27 paper.tex
11 paper.bib
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@@ -536,3 +536,14 @@ @article{Rappe:1992um
Number = {25},
Pages = {10024-10035},
}
+
+@Article{NWChem,
+ Author = "M. Valiev and E. J. Bylaska and N. Govind and K. Kowalski and T. P. Straatsma and H. J. J. {van Dam} and D. Wang and J. Nieplocha and E. Apra and T. L. Windus and W. A. {de Jong}",
+ Title = "NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations",
+ Journal = "Comput. Phys. Commun.",
+ Volume = "181",
+ Number = "9",
+ Pages = "1477–1489",
+ doi = "10.1016/j.cpc.2010.04.018",
+ year = 2010
+}
BIN  paper.pdf
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53 paper.tex
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@@ -148,7 +148,7 @@
Geoffrey R Hutchison$^4$%
\email{Geoffrey R Hutchison - geoffh@pitt.edu}
\and
- Karol M Langner$^5$%
+ Karol M Langner$^5$%
\email{Karol M Langner - langnerkm@chem.leidenuniv.nl}
\and
Daniel M Lowe$^6$%
@@ -169,15 +169,15 @@
Christoph Steinbeck$^{10}$%
\email{Christoph Steinbeck - steinbeck@ebi.ac.uk}
\and
- Adam L Tenderholt$^{11}$%
+ Adam L Tenderholt$^{11}$%
\email{Adam L Tenderholt - adamlt82@u.washington.edu}
\and
Kevin J Theisen$^{12}$%
- \email{Kevin J Theisen - kevin@ichemlabs.com}
+ \email{Kevin J Theisen - kevin@ichemlabs.com}
\and
Egon L Willighagen$^{13}$%
\email{Egon L Willighagen - egon.willighagen@ki.se}
- }
+}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -187,19 +187,20 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\address{%
- \iid(1)Division of Molecular Toxicology, Institute of Environmental Medicine, %
- Nobels vaeg 13, Karolinska Institutet, 171 77 Stockholm, Sweden\\
- \iid(2)National Institute of Health, Somewhere in the US, USA\\
- \iid(5)Analytical and Biological Chemistry Research Facility, Cavanagh Pharmacy Building, University College Cork, College Road, Cork, Co. Cork, Ireland\\
- \iid(6)Cheminformatics and Metabolism Team, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK\\
- \iid(7)Unilever Centre for Molecular Sciences Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK\\
- \iid(8)GGA Software Services LLC, 41 Nab. Chernoi rechki 194342, Saint Petersburg, Russia\\
\iid(1)Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden \\
- \iid(10)Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA\\
- \iid(3)NIH, Somewhere in the US, USA\\
- \iid(12)iChemLabs, 200 Centennial Ave., Suite 200, Piscataway, NJ 08854, USA \\
- \iid(13)Gorlaeus Laboratories, Leiden University, 2333 CC Leiden, The Netherlands \\
- \iid(14)Department of Chemistry, University of Washington, Seattle, WA 98195
+ \iid(2)National Institute of Health, Somewhere in the US, USA \\
+ \iid(3)... \\
+ \iid(4)Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA \\
+ \iid(5)Gorlaeus Laboratories, Leiden University, 2333 CC Leiden, The Netherlands \\
+ \iid(6)Cheminformatics and Metabolism Team, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK \\
+ \iid(7)Unilever Centre for Molecular Sciences Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK \\
+ \iid(8)Analytical and Biological Chemistry Research Facility, Cavanagh Pharmacy Building, University College Cork, College Road, Cork, Co. Cork, Ireland \\
+ \iid(9)GGA Software Services LLC, 41 Nab. Chernoi rechki 194342, Saint Petersburg, Russia \\
+ \iid(10)... \\
+ \iid(11)Department of Chemistry, University of Washington, Seattle, WA 98195 \\
+ \iid(12)iChemLabs, 200 Centennial Ave., Suite 200, Piscataway, NJ 08854, USA \\
+ \iid(13)Division of Molecular Toxicology, Institute of Environmental Medicine, %
+ Nobels vaeg 13, Karolinska Institutet, 171 77 Stockholm, Sweden
}%
\maketitle
@@ -437,24 +438,22 @@ \subsection*{Computational chemistry analysis}
quantum chemistry calculations and in interpreting their results.
Electronic structure calculations have a long tradition in the
chemistry community and a variety of programs exist, mostly
-proprietary software with the notable exception of NWChem.
+proprietary software with the notable exception of NWChem.\cite{NWChem}
However, since each program uses different input formats, and the
results are output differently even varying between different versions
-of the software, preparing calculations and extracting the results in
-an automated way is problematic.
+of the software, preparing calculations and automatically extracting
+the results is problematic.
-Avogadro has already been mentioned as a GUI for preparing
-computational chemistry calculations. It uses Open Babel to read the
-output of several electronic structure packages, and also to write the
-input files for each. Jmol (see below) can also depict computational
-chemistry results including molecular orbitals.
+Avogadro has already been mentioned as a GUI for preparing calculations.
+It uses Open Babel to read the output of several electronic structure
+packages, and also to write the input files for each. Jmol (see below)
+can also depict computational chemistry results including molecular orbitals.
In 2006, the Blue Obelisk project cclib~\cite{cclib} was established
with the goal of parsing the output from computational chemistry
programs and presenting it in a standard way so that further analyses
-could be carried out independently of the quantum package used to
-obtain the results. cclib is a Python library, and
-the current version (version 1.0.1)
+could be carried out independently of the quantum package used.
+cclib is a Python library, and the current version (version 1.0.1)
supports 8 different computational chemistry codes and extracts over
30 different calculated attributes. Two related BO projects build upon
cclib. GaussSum~\cite{WebGaussSum},
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