combichem.blogspot.com

computerandchemistry.blogspot.com

Comp and Chem: Calculate RMSD from two XYZ files

http://computerandchemistry.blogspot.com/2013/04/calculate-rmsd-from-two-xyz-files.html

Masters student in Computational Chemistry at University of Copenhagen, writing about what I feel like. Enjoy the reading. Friday, 26 April 2013. Calculate RMSD from two XYZ files. Calculating the RMSD mathematically for two sets of xyz coordinates for $n$ particles is straight forward:. Mathrm{RMSD}(v,w) = sqrt{ frac{1}{n} sum {i=1} n ( v {ix} - w {ix}) 2 (v {iy} - w {iy}) 2 (v {iz} - w {iz}) 2 ) }$. Http:/ en.wikipedia.org/wiki/Kabsch algorithm. The algorithm is nicely written out on wikipedia, so it w...

computerandchemistry.blogspot.com

Comp and Chem: November 2012

http://computerandchemistry.blogspot.com/2012_11_01_archive.html

Masters student in Computational Chemistry at University of Copenhagen, writing about what I feel like. Enjoy the reading. Monday, 26 November 2012. PM6 in GAMESS, Part 3, a new file is introduced. This was great, but it also meant I had to start over with respect to mapping and compiling of this file. The mndod.f, for historical purpose, is the d-integrals from the old mndo-d method (created by Walter Theil), and then converted to work with MOPAC from version 7 , for AM1-D and on. After working a weeks ...

computerandchemistry.blogspot.com

Comp and Chem: Setting up a computational cluster (HPC), part 2

http://computerandchemistry.blogspot.com/2015/06/setting-up-computational-cluster-hpc_11.html

Masters student in Computational Chemistry at University of Copenhagen, writing about what I feel like. Enjoy the reading. Thursday, 11 June 2015. Setting up a computational cluster (HPC), part 2. Now that we can easily provide DHCP, DNS and TFTP and a debian image for all the nodes, we want to make it easy to maintain the cluster and setup user management. For maintaining packages and configuration etc we use Puppet on Debian. So awesome! Otherwise puppet agent will not know where to connect. Bin/bash e...

pythonchem.blogspot.com

Python, Chemistry and Other Stuff: November 2011

http://pythonchem.blogspot.com/2011_11_01_archive.html

Python, Chemistry and Other Stuff. I'll blog about python, its use in chemistry and other stuff I find interesting. Wednesday, November 30, 2011. Cut'n'Frag: Fragment smart using SMARTS. In our research group. Part of the research we do is method development. To facilitate these new methods, tools are often required to setup various calculations or treat output files. Some of this research[ 1. Is in fragment based methods[ 2. This post is about one key aspect of FragIt: How to use Open Babel[ 4. Basicall...

pythonchem.blogspot.com

Python, Chemistry and Other Stuff: December 2011

http://pythonchem.blogspot.com/2011_12_01_archive.html

Python, Chemistry and Other Stuff. I'll blog about python, its use in chemistry and other stuff I find interesting. Wednesday, December 7, 2011. Obtaining Contact Numbers using SMARTS. Because I'm on a roll with blogging right now and I am looking for excuses to not write the next paper, here is a post about how to utilize SMARTS[ 1. For something cheminformatically-vant such as the contact number[ 2. We will base the new code on what I did in the last post I wrote. Import openbabel filename = "1CRN....

computerandchemistry.blogspot.com

Comp and Chem: PM6 in GAMESS, Part 3, a new file is introduced

http://computerandchemistry.blogspot.com/2012/11/pm6-in-gamess-part-3-new-file-is.html

Masters student in Computational Chemistry at University of Copenhagen, writing about what I feel like. Enjoy the reading. Monday, 26 November 2012. PM6 in GAMESS, Part 3, a new file is introduced. This was great, but it also meant I had to start over with respect to mapping and compiling of this file. The mndod.f, for historical purpose, is the d-integrals from the old mndo-d method (created by Walter Theil), and then converted to work with MOPAC from version 7 , for AM1-D and on. After working a weeks ...

computerandchemistry.blogspot.com

Comp and Chem: PM6 in GAMESS, Part 1

http://computerandchemistry.blogspot.com/2012/08/pm6-in-gamess-part-1.html

Masters student in Computational Chemistry at University of Copenhagen, writing about what I feel like. Enjoy the reading. Tuesday, 28 August 2012. PM6 in GAMESS, Part 1. Okay, so I'm working on implementing the semi-empirical method PM6 (by Jimmy "Mopac" Stewart) in GAMESS-US. Delta H f = E { rm Elect} E { rm Core} - sum {A} {} E {el} {A} sum {A} {} Delta H {f} {A}$. E n(A,B) = Z A Z B langle s A s A s B s B rangle left ( 1 e {- alpha A R {AB} e {- alpha B R {AB} right ) $. Okay, but is this better?

computerandchemistry.blogspot.com

Comp and Chem: PM6 in GAMESS, Part 2

http://computerandchemistry.blogspot.com/2012/08/pm6-in-gamess-part-2.html

Masters student in Computational Chemistry at University of Copenhagen, writing about what I feel like. Enjoy the reading. Friday, 31 August 2012. PM6 in GAMESS, Part 2. Okay, so I'm still working on implementing PM6 integrals in GAMESS. I got the source code from MOPAC 7.1 which includes d. Integrals for the MNDO-D method (which is what Jimmy Stewart is using for PM6 in the newest MOPAC (hopefully), which originates from a program written by Walter Thiel). So the strategy is simply. The map for MOPAC is:.

computerandchemistry.blogspot.com

Comp and Chem: August 2012

http://computerandchemistry.blogspot.com/2012_08_01_archive.html

Masters student in Computational Chemistry at University of Copenhagen, writing about what I feel like. Enjoy the reading. Friday, 31 August 2012. PM6 in GAMESS, Part 2. Okay, so I'm still working on implementing PM6 integrals in GAMESS. I got the source code from MOPAC 7.1 which includes d. Integrals for the MNDO-D method (which is what Jimmy Stewart is using for PM6 in the newest MOPAC (hopefully), which originates from a program written by Walter Thiel). So the strategy is simply. The map for MOPAC is:.