CRASY

Correlated Rotational Alignment Spectroscopy

Scientific Writing

Writing scientific publications seems to be a science on its own for most of young researchers, but there is no magic behind scientific writing! By following simple rules, everybody can improve his writing skills. I summarized these rules in a cheat sheet for scientific writing.

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Of course, you should not expect a miracle. Your principal investigator will always find something to complain about. ūüėČ

If you want to read further on The Science of Scientific Writing, please refer to the article.

Ab initio code for starters

Ab initio packages for starters

 PCGamess: Ab initio code for your Windows PC
MacMolPltIcon  MacMolplt: Nice visualization of Gamess output
arguslab  Arguslab: Visualize or draw molecules, optimize with molecular dynamics, useful to generate starting geometries
MOPAC2012  Mopac: Molecular dynamics and semiempirical methods

 

Suggested sequence for simple structure calculations:

(1) Draw¬†your molecule in¬†CHEMSKETCH and push the ‘optimize 3D’ button, save it in .mol format

(2) I used OPENBABEL to convert the .mol coordinates to Gamess input format.

(3) Perform a PM3 calculation in Gamess Firefly to get a better structure (fast calculation). A sample input file is here: Toluene_PM3_geometry.

(4) Use the PM3 structure result to start a DFT (B3LYP) calculation with the Gaussian 6-31 basis set (fraction of a minute calculation). A sample input file is here: Toluene_B3LYP-6-31G_geometry.

(5) Use the DFT-6-31 structure result to start a DFT B3LYP calculation with a larger basis set (e.g.,Dunnings augmented correlation-consistent valence-triple-zeta basis set. This basis is about as good as it gets, so this will be the final structure.) A sample input file is here: Toluene_B3LYP-accpVTZ_geometry.

Latex enviroment plugin running

Dear users of crasy.org,

a latex enviroment plugin is activated to allow for formula expression everywhere on this website, even in comments. The only thing you have to do is to embed the latex code in a \char36 (add your code here)¬†\char36 enviroment. Have fun using latex, since¬†it also helps to write greek letters like \Delta or to generate indices for letters like t_1. And don’t forget to use google, if you want to find any latex code¬†ūüėČ …