Dear members of the ACS community, As a sequel of the previous document "Some Simulation Software" I would like to share a potpourri of some of the interesting visualization software I have encountered and worked with. As always, I hope that theoretical chemists could share their experiences with some of them and feel free to expand this short list. Following is a summary, that will be completed and improved at a later date (it surely contain some mistakes and should be considered as nothing more than a draft for now). Software (& link) License Free Source Dev Release date version Language MM FF 1 One interest (subjective) AVOGADRO GPL Y Y 2016-06 v1.2.0 Py C++ Y Available, complete package. CHEMOFFICE COM N 2 N 2018-04 v17.1 ? Y 2D structure editing, complete. GABEDIT SITE/BSD Y Y 2017-07 v2.5.0 C Y batch interface with many codes. GDIS GPL Y Y 2015-02 v0.91 C N easy to contribute, and fast 3 . GHEMICAL GPL Y Y 2011-10 v3.0.0 C++ Y interface with mpqc, 3D MM. JMOL LGPL Y Y 2018-06 v14.29.17 JAVA N can be embedded in web pages. MOLDEN SITE/COM N 4 N 2018-05 v5.8 F Y integration with Gaussian. PLATON SITE N 5 N 2018-06 - C F95 Y best B&W chemical structures. POWDERCELL SITE N 5 N 2000s v2.4 Pasc. N old 6 , simple XRD pattern to structure. RASMOL GPL Y Y 2011-05 v2.7.5.2 C N simple display program. VESTA SITE N 7 N 2018-03 v3.4.4 C++ N crystal generation. VMD SITE Y N 8 2016-11 v1.9.3 C++ CUDA Y GPU acceleration, plugins. XCRYSDEN GPL Y N 2014-06 v1.5.60 C F N display primitive Brillouin zone 1 Molecular Mechanics / Force Field: Allows to quickly optimize a "hand drawn" molecule into a reasonable structure. 2 Some trial software program (for 14 days) exists. 3 As a disclaimer, I am currently collaborating on the elaboration of GDIS. 4 Free for non-profit organizations and academic users. 5 Free for academic use. 6 While the software dates from 2000s it is still widespread and cited in 2018, (also a good educational material). 7 Free for academic, scientific, educational, and non-commercial users. 8 CVS access on request only. Glossary: Licenses: COM - commercial SITE - on-site license GPL - general public license LGPL - lesser GPL BSD - Berkley software distribution Language: F - FORTRAN language (usually a mix with 77 and 90 version) C - C language C++ - C++ language Py - Python language Pasc. - Pascal language CUDA - NVIDIA GPGPU language I really hope that, similarly to the previous document, you will find this content to be of interest among ACS community. -- Hubert OKADOME VALENCIA
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Would anyone be interested in either of these topics? Impurities and secondary metabolites are the major concern. A genetic engineering puzzle? #NK-92 Donations only. Need library access.
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Dear ACS member, As a theoretical chemistry student, and also at a later stage, I often encounter some difficulties in finding some central place to access important information such as: * international job opportunities; * conferences, meetings, workshops; * latest developments in the field... Today I would like to introduce the , computational chemistry list (also known as simply CCL) which job posting and conference page have proved useful for me during years. CCL use to be backed by the COMP division of ACS, which you might already have heard about. Besides ACS (of course) there are surely some other interesting places where you can find this kind of information. Please let us know in the comments if you happen to know a good one Sincerely, -- Hubert OKADOME VALENCIA
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Density functional theory (DFT) is a powerful technique used in theoretical chemistry (and physics) that unfortunately can be quite difficult to explain. A short (yet complete) introduction to DFT is given by Klaus Capelle as a very nice, freely accessible, educational material. https://arxiv.org/abs/cond-mat/0211443 It also happen to be one of my favorite teaching material! Any noteworthy educational contents about theoretical chemistry? Please let us know!
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Dear members of ACS community, I though it would be nice if theoretical chemists could share a compilation of some interesting simulation software. This is why I propose this - admittedly quite small - list of some of the codes I have been using or that I have worked with. Please feel free to expand or correct this document and/or to provide some new information*. Following is a summary, that will be completed and improved at a later date (it surely contain some mistakes and should be considered as nothing more than a draft for now). Software (and link) License Free Source dev Release date version Language Theory (main function) one interest (subjective) ABINIT GPL Y Y 2018-04 v8.8 F03 PW DFT, GW easy to contribute & complete CASTEP COM 1 N 1 N 2 2018-04 v18.1 F03 PW DFT included in Material Studio CP2K GPL Y Y 2018-06 v6.1 F03/CUDA GAPW DFT, SE, FF QM/MM possible DL_POLY_C DL_POLY_4 BSD COM Y N 3 Y N 3 2017-03 v1.10 2016-03 v4.08 F90 F90 MM FF MM FF popular MD package GAMESS(UK) GAMESS(US) COM SITE N 1 Y 4 N 1 Y 4 2010-01 v7.0 2018-02 18R1 C F C F HF, DFT, SE, GW HF, DFT, SE QM/MM w/ CHARMM QM/MM w/ TINKER GAUSSIAN COM 5 N N 6 2018-03 16-B01 C F CUDA HF, DFT, SE, FF wildly used and complete GROMACS LGPL Y Y 2018-06 2018-2 C C++ GPU MM FF very fast parallel code GULP SITE Y 3 Y 3 2018-01 v5.0 F90 0~3D MM FF fast and periodic MPQC LGPL Y Y 2006-03 v2.3.1 C++ C F HF DFT massively parallel & available NAMD SITE Y 3 Y 3 2016-12 v2.12 C++ CUDA MM FF fast MD OPENMX GPL Y Y 2016-04 v3.8 C pAO DFT very complete package Q-ESPRESSO GPL Y Y 2017-12 v6.2.1 F95 PW DFT pseudo-potential database SIESTA GPL Y Y 2017-07 v4.0.1 F95 pAO DFT order-N TINKER SITE Y 7 Y 7 2018-02 v8.4 F95 CUDA MM FF a reference in FF VASP COM N Y 8 2017-04 v5.4.4 F90 CUDA PW DFT, GW very fast and reliable 9 1 There is an academic free program in UK. 2 Source cannot be accessed outside Europe except for some very specific collaboration (source: private communication). 3 Free for academic use only. 4 Free for academic and industrial use after email-registration. 5 Gaussian have been known in the past to enforce a severe licensing. 6 Source available under paid license. 7 Free for non-commercial use. 8 Distributed as source. 9 I have been using this code daily since 2002 so I might be a little partial... Glossary: Licenses: COM - commercial SITE - on-site license GPL - general public license LGPL - lesser GPL BSD - Berkley software distribution (2-clause) Language: F03 - FORTRAN 2003 language F90 - FORTRAN 90 language (sometimes incorrectly used for F95) F95 - FORTRAN 95 language F - FORTRAN language (usually a mix with 77 and 90 version) C - C language C++ - C++ language CUDA - NVIDIA GPGPU language openCL - AMD GPGPU language GPU - both CUDA and openCL Theory: PW: plane-wave basis pAO: pseudo atomic orbitals basis MD: molecular dynamics HF: Hartree Fock DFT: density functional theory GW: Green's function SE: semi-empiric MM: molecular mechanics FF: classical force field QM/MM: quantum mechanics / molecular mechanics I hope you will find this content interesting and I will propose soon the same kind of information concerning visualization software. -- Hubert OKADOME VALENCIA * I especially like to know about local, often very specialized, codes for which development is unfortunately quite often confidential and limited to one university. This codes are often shared within a group or two, while there would be a great interest into making them wild-known.
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