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...
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:.
computerandchemistry.blogspot.com
Comp and Chem: Setting up a computational cluster (HPC), part 1
http://computerandchemistry.blogspot.com/2015/06/setting-up-computational-cluster-hpc.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 1. Which practically means I had to set it up from scratch. And a lot of googling. So much googling. So here is what I did. To speed things up, the whole installation is done via a local apt-get mirror on the master node. This also insures that all the packages are exactly the same version. Hosts home folder (for ...
computerandchemistry.blogspot.com
Comp and Chem: February 2014
http://computerandchemistry.blogspot.com/2014_02_01_archive.html
Masters student in Computational Chemistry at University of Copenhagen, writing about what I feel like. Enjoy the reading. Monday, 17 February 2014. Compiling and setting up GAMESS. Small guide on how to setup the QM software GAMESS. On a normal Ubuntu computer and work in parallel with multiple nodes (via sockets). Loosely this is based on this guide on how to compile GAMESS. 1 Download the newest GAMESS. And answer the questions. Answer them truthfully. Note: Compiling without Math library. Now we just...
computerandchemistry.blogspot.com
Comp and Chem: April 2013
http://computerandchemistry.blogspot.com/2013_04_01_archive.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...
