Chemistry

See here for compiling computational software:http://verahill.blogspot.com.au/p/compilinginstalling-software-for.html.

There's an enormous back-log of posts to add, so don't forget to use google too.
514. Extracting Frequency data from a gaussian 09 calculation for gnuplot
513. Extracting data from a PES scan with gaussian
512. Briefly: zmatrices in nwchem -- methanol
511. When nwchem PES scans fail to constrain -- autoz failure
506. Extracting optimized structures from a potential energy scan in nwchem
503. (relaxed) PES scanning in Nwchem revisited.
499. Briefly: Drawing NMR sequences using metapost and Mark White's pulse.mp
498. Briefly: Drawing NMR pulse sequences using APSEQ and Mathematica
486. MS data, part IV: Making a stacked spectrum plot using gnuplot
483. MS data, part III: generating a matrix by combining several spectra, and plotting it in gnuplot
483. MS data, part III: generating a matrix by combining several spectra, and plotting it in gnuplot
480. MS data, part II. Plotting and comparing with predicted isotopic enveloped
477. OpenChrom - Dempster
474. MS data, part I: Exporting data as csv from wsearch32, and generating MS assignments using Matt Monroe's molecular weight calculator
462. Olex2 (1.1) on Debian
461. Briefly: setting up SHELX on linux (crystallography)
460. Briefly: Crystallography software: CCSD Mercury
458. Briefly: Converting GRAMS ASP ascii data to two-column ascii data
446. B3LYP and WAH -- the confusion
439. Calculate frequencies from a hessian file from NWChem: example in Octave (matlab)
415. Briefly: making a polyhedral figure in gdis
396. Compiling gromacs 4.6 with gpu support, openblas and fftw3 on debian wheezy
390. NWChem: "Fix collapse/expand in xc_nucder_gen" when using actlist and frequency calc
389. Patches for NWChem 6.1.1 on Debian Wheezy/Testing
388. NWChem, PSPW and Fortran runtime error
380. Modifying NWChem code without a full recompile
363. Generating an image in PyMol
337. Modifying Nwchem 6.1.1 to work with GabEdit
325. Compiling ECCE 6.4 on Debian Testing
318. qmol -- a molecular weight calculator for linux.
294. Bruker 1D processing using octave/matlab
285. Minor bug in ECCE
281. Visualising NWChem output with GabEdit
280. gOpenMol on Debian Wheezy
273. NWChem and COSMO: custom radii
265. shmmax revisited -- and shmall, shmmni
252. Molecular weight calculator in python
251. Isotopic pattern calculator in python
243. My own personal benchmarks for NWChem, gromacs with atlas, openblas, acml on AMD and Intel.
241. pKa, part 3: ccCA in NWChem. Doing something wrong?
240. Harmonic frequency scaling in NWChem
236. Calculating pKa, part 1: Example (attempt) of an isodesmic reaction in NWChem
227. New compute node using AMD FX 8150. Gromacs, nwchem performance and benchmarks.
202. Reproducing the paper: computing organic reduction potentials
198. NWChem -- freeze core and tddft on benzene
195. Frequency calcs in nwchem
190. In deep water: NWChem and COSMO
165. Approach to computing reorganisational energies using nwchem
164. A rough approach to calculating redox potentials using dft
162. PSPW/Carr-Parrinello using ECCE
159. PES scanning of methanol bonds, angles, torsion using nwchem, nwgeom and python
157. Restarting gaussian (g09) job on an SGE system (qsub)
145. Rasmol on ROCKS 5.4.3
143. MD =Ecce + NWChem. 4.Dynamics
142. MD = Ecce + NWChem. 3. Energy
141. MD = Ecce + NWChem. 2. MD Optimize
140. MD = ECCE + NWChem: 1. Prepare
137. Setting up Gaussian g09 on debian --precompiled binaries
135. Oniom in Gaussian --with a little bit of help from gromacs and openbabel
177. Jerry-rigging g09 UV/VIS spectra in gnuplot and/or octave
113. Using ECCE to run NWChem jobs
111. ECCE (NWChem) on Debian, and ROCKS (CentOS)
56. Gromacs -- setting up and running energy minimisation of methanol in water. Using itp files
53. GROMACS -- carbon dioxide in water. Example