Monday, February 8, 2016

DFTB3 in GAMESS

I recently did my first DFTB3 calculations in GAMESS.  The process wasn't completely obvious, hence this post.

First I got the parameter files from dftb.org.  You have to fill in and email a registration form to get a login so that might take a few days.  I downloaded the 3ob-3-1 parameter set.

The DFTB3-related input can be found below.  My molecule contains C, N, O, and H atoms.  If there are additional atoms then you need to define additional pairs.  It is OK to specify atom pairs for atoms that are not in the molecule, so the easiest might be to define all relevant pairs once and for all and use it in all input files.

The value for dampex and hubder are found in the README file that is located in the 3ob-3-1 folder I downloaded.  hubder defines parameters for N, C, O, and H - in that order.  It was not clear from the manual what the order should be.  I found the correct order by running the input file without hubder. This run prints out the default hubder values in the order  N, C, O, and H and it turns out that is the order you need to use in the input file.

 $basis gbasis=dftb $END
 $dftb ndftb=3 DAMPXH=.t. dampex=4.0
       hubder(1)=-0.1535,-0.1492,-0.1575,-0.1857 $end
 $dftbsk
 C C "/Applications/gamess/3ob-3-1/C-C.skf"
 C H "/Applications/gamess/3ob-3-1/C-H.skf"
 C N "/Applications/gamess/3ob-3-1/C-N.skf"
 C O "/Applications/gamess/3ob-3-1/C-O.skf"
 H C "/Applications/gamess/3ob-3-1/H-C.skf"
 H H "/Applications/gamess/3ob-3-1/H-H.skf"
 H N "/Applications/gamess/3ob-3-1/H-N.skf"
 H O "/Applications/gamess/3ob-3-1/H-O.skf"
 N C "/Applications/gamess/3ob-3-1/N-C.skf"
 N H "/Applications/gamess/3ob-3-1/N-H.skf"
 N N "/Applications/gamess/3ob-3-1/N-N.skf"
 N O "/Applications/gamess/3ob-3-1/N-O.skf"
 O C "/Applications/gamess/3ob-3-1/O-C.skf"
 O H "/Applications/gamess/3ob-3-1/O-H.skf"
 O N "/Applications/gamess/3ob-3-1/O-N.skf"
 O O "/Applications/gamess/3ob-3-1/O-O.skf"
 $end

I would like to thank +Anders Steen Christensen for his help in figuring this out.


This work is licensed under a Creative Commons Attribution 4.0

Friday, January 1, 2016

Computational Chemistry Highlights: December issue

The December 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 scientists. You can read more about it here.

Table of content for this issue features contributions from CCH editors Steven Bachrach, David Bowler, Grant Hill and Jan Jensen:

Scalable Quantum Simulation of Molecular Energies






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Also, for your daily computational chemistry fix subscribe to Computational Chemistry Daily


This work is licensed under a Creative Commons Attribution 4.0

Tuesday, December 1, 2015

Computational Chemistry Highlights: November issue

The November 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 scientists. You can read more about it here.

Table of content for this issue features contributions from CCH editors Steven Bachrach, Christoph Jacob and Jan Jensen:

Enhancing NMR Prediction for Organic Compounds Using Molecular Dynamics

Tetrabenzo[a,f,j,o]perylene: A Polycyclic Aromatic Hydrocarbon With An Open-Shell Singlet Biradical Ground State

Molecular Dynamics of the Diels–Alder Reactions of Tetrazines with Alkenes and N2 Extrusions from Adducts

Dual-Cavity Basket Promotes Encapsulation in Water in an Allosteric Fashion

Switching between Aromatic and Antiaromatic 1,3-Phenylene-Strapped [26]- and [28]Hexaphyrins upon Passage to the Singlet Excited State

A Local Variant of the Conductor-Like Screening Model for Fragment-Based Electronic-Structure Methods

Interested in more? There are many ways to subscribe to CCH updates.

Also, for your daily computational chemistry fix subscribe to Computational Chemistry Daily


This work is licensed under a Creative Commons Attribution 4.0

Sunday, November 22, 2015

Quick way to share interactive molecular structures and animations


Here is a neat trick I learned from @gyges01 on Twitter.  Say you want to share an interactive molecular structure or animation with someone not well versed in structural visualization tools. Here's what you do.

1. Put your file on a server like figshare and copy the link. For example: http://files.figshare.com/1860026/ethen_01oIRC.cml
Unfortunately, a dropbox link, which would have been even easier, does not seem to work. See below

2. Combine this link with "http://chemapps.stolaf.edu/jmol/jmol.php?source=":
http://chemapps.stolaf.edu/jmol/jmol.php?source=http://files.figshare.com/1860026/ethen_01oIRC.cml

3. Email (or Tweet) the link (takes a minute to load) with instructions to start animation: right-click > animation > play

4. You can autostart the animation by uploading a "dummy" xyz file with the commands: http://chemapps.stolaf.edu/jmol/jmol.php?source=http://files.figshare.com/2367420/ethen_test.xyz

ethen_test.xyz looks like this:

1
jmolscript: load http://files.figshare.com/1860026/ethen_01oIRC.cml; animation on; animation mode palindrome;
h 0.0 0.0 0.0

2015.11.23 Update Twitter strikes again: @aminophen found the trick to making this work with Dropbox.  Change https://www.dropbox.com/s/xxx/file?dl=0 to http://dl.dropboxusercontent.com/s/xxx/file.  Example:
https://www.dropbox.com/s/t42dx22mxsioja6/ethen_test.xyz?dl=0 to http://dl.dropboxusercontent.com/s/t42dx22mxsioja6/ethen_test.xyz and use it like before: http://chemapps.stolaf.edu/jmol/jmol.php?source=http://dl.dropboxusercontent.com/s/t42dx22mxsioja6/ethen_test.xyz



This work is licensed under a Creative Commons Attribution 4.0

Sunday, November 1, 2015

Computational Chemistry Highlights: October issue

The October 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 scientists. You can read more about it here.

Table of content for this issue features contributions from CCH editors Steven Bachrach, David Bowler and Jan Jensen:

Stochastic Multiconfigurational Self-Consistent Field Theory




The accuracy of semi-local functionals

Interested in more? There are many ways to subscribe to CCH updates.

Also, for your daily computational chemistry fix subscribe to Computational Chemistry Daily


This work is licensed under a Creative Commons Attribution 4.0

Thursday, October 1, 2015

Computational Chemistry Highlights: September issue

The September 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 scientists. You can read more about it here.

Table of content for this issue features contributions from CCH editors Steven Bachrach and Jan Jensen:

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum