O.K. I have finished my MD or EPSR calculations, now what?
The software ANGULA (glass eel in english) tries to solve this question offering a set of tools to calculate from localized Radial Distribution Functions (in a specific direction) to Spatial Density Maps. The software is written in a way that at every step all the calculations are accesible (there are no "internal" results). This is done to offer an extremely flexibility so you can "step out" from ANGULA at any point by plugging the result in any other software. This is done at expenses of occupying memory in your computer, but fortunately, nowadays this is not such a big problem.
The program is written in plain fortran90, is an open code so that you can add any function you want. The calls to the system are written for windows and Linux systems, and it seems to work in Mac. The binaries are only available for windows. The graphics are simply displayed using gnuplot (ANGULA simply calls this program every time you want to see a graph) and molecules are displayed using VMD, these two programs are thus very useful if you want to angulize your configurations .
WARNING: if you have used already, the version now in dropbox is NEW. The main difference being the format of configuration file and some changes in traductor. Now ANGULA does not add thausends of pseudoatoms, which is a nice thing. Also the configuration file is much more clear (at least to my eyes!). Finally, thanks to the new configuration file format, the mixture file is not needed anymore, this makes things much simpler.
This figure is produced using ANGULA with VMD and GNUPLOT software to produce the nice drawings. In the upper pannel you can see the probability "maps" related to the position of the first four molecules of water (left) and Carbon Tetrachloride (right) in spherical coordinates. In the lower panel the same information is shown, but in this case as Spatial Density Maps.
- (link to Dropbox)
- (if link doesn't work: www.dropbox.com/sh/mdia85ch99bamyo/AAAsctyOvtlwkFkjM2Lw9t9la?dl=0)
- DOWNLOAD example (link to DropBox)
- (if link doesn't work: https://www.dropbox.com/sh/9a2o4hl7sks7l89/AACUUZ2VW146xT3-6eJw75Gna?dl=0)
And the auxiliary programs
- Gnuplot (to plot amazing graphs)
- VMD to produce extraordinary figures
- Rasmol (windows) or Jmol to see molecules
- Gfortran to compile the program (If you want to. An executable for windows is ready to use)
Papers released using ANGULA
- The structure of liquid water beyond the first hydration shell
A. Henao, S. Busch, E. Guàrdia, J. Ll. Tamarit, L. C. PardoPhysical Chemistry Chemical Physics 18, 1420-1425 (2016)
- A continuous mixture of two different dimers in liquid water
LC Pardo, A Henao, S Busch, E Guàrdia, JL TamaritPhysical Chemistry Chemical Physics 16 (44), 24479-24483 (2014)
- On the positional and orientational order of water and methanol around indole: a study on the microscopic origin of solubility
A. Henao, A. J. Johnston, E. Guàrdia, S. E. McLain and L. C. PardoPhysical Chemistry Chemical Physics 18, 23006-23016 (2016)
- Specific effects of monovalent counterions on the structural and interfacial properties of dodecyl sulfate monolayers
D. T. Allen, Y. Saaka, L. C. Pardo, M. J. Lawrenceb and C. D. LorenzPhysical Chemistry Chemical Physics 18, 30394-30406(2016)
- Microstructures of negative and positive azeotropes
J. J. Shephard, S. K. Callear, S. Imberti, J. S. O. Evans and C. G. SalzmannPhysical Chemistry Chemical Physics 18, 19227 (2016)
- On the atomic structure of cocaine in solution
Johnston, A. J., Busch, S., Pardo, L. C., Callear, S. K., Biggin, P. C. and McLain, S. E.Physical Chemistry Chemical Physics 19, 991-999 (2016)
- Atomic scale insights in to urea-peptide interactions in solution
Steinke, N., Gillams, R. J., Pardo, L. C., Lorenz, C. D. and McLain, S. E.Physical Chemistry Chemical Physics 18, 3862-3870 (2016)
- Characterizing ordering in liquids: An information theoretic approach
LC Pardo, A Henao, A Vispa
Journal of Non-Crystalline Solids 407, 220-227 (2015)
- Amphipathic Solvation of Indole: Implications for the Role of Tryptophan in Membrane Proteins
AJ Johnston, YR Zhang, S Busch, LC Pardo, S Imberti, SE McLainThe Journal of Physical Chemistry B (2015)
- Short-range interactions of concentrated proline in aqueous solution
S Busch, CD Lorenz, J Taylor, LC Pardo, SE McLainThe Journal of Physical Chemistry B 118 (49), 14267-14277 (2014)
- On the structure of water and chloride ion interactions with a peptide backbone in solution
S Busch, L.C. Pardo, WB O'Dell, CD Bruce, CD Lorenz, SE McLainPhysical Chemistry Chemical Physics 15 (48), 21023-21033 (2013)
- Solvation and Hydration of the Ceramide Headgorup in a non-polar solution.
R Gillams et al.
J. Phys. Chem. B, 2015, 119 , pp 128–139 (2014)
- Short range order of CCl4: RMC and MD Methods
A Silva-Santisteban, A Henao, S Pothoczki, FJ Bermejo, JL Tamarit, ...Journal of Physics: Conference Series 549 (1), 012014 (2014)
- Competing structures within the first shell of liquid C2Cl6: a molecular dynamics study
A Henao, S Pothoczki, M Canales, E Guardia, LC PardoJournal of Molecular Liquids 190, 121-125 (2014)
- Insights into the determination of molecular structure from diffraction data using a Bayesian algorithm
A Henao, M Rovira-Esteva, A Vispa, JL Tamarit, E Guardia, LC PardoJournal of Physics: Condensed Matter 25 (45), 454217 (2013)
- Comparison of the atomic level structure of the plastic crystalline and liquid phases of CBr2Cl2: neutron diffraction and reverse Monte Carlo modelling
S Pothoczki, L Temleitner, LC Pardo, GJ Cuello, M Rovira-Esteva, ...Journal of Physics: Condensed Matter 25 (45), 454216 (2013)
- Differences in first neighbor orientation behind the anomalies in the low and high density trans-1, 2-dichloroethene liquid
M Rovira-Esteva, NA Murugan, LC Pardo, S Busch, JL Tamarit, GJ Cuello, ...The Journal of chemical physics 136 (12), 124514 (2012)
- Microscopic structures and dynamics of high-and low-density liquid t r a n s-1, 2-dichloroethylene
M Rovira-Esteva, A Murugan, LC Pardo, S Busch, MD Ruiz-Martin, ...Physical Review B 81 (9), 092202 (2010)
- Role of steric and electrostatic effects in the short-range order of quasitetrahedral molecular liquids
L Pardo, JL Tamarit