Centered gas-phase structuresMon Dec 19 11:49:13 CET 2016
The structures for all gas phase molecules were centered in a box of 10x10x10 nm in order to prevent issues when simulating them. In the original version the structures were the output of long vacuum simulations that were not necessarily inside this box.
Downloadable Amber and Charmm filesThu Nov 17 15:56:32 2016
From now on you can download files for AMBER or CHARMM from select molecule pages (the ones where we performed liquid calculations). Complete packages can be downloaded in zip archives from the force field page.
Corrected GAFF structuresMon Nov 14 10:02:07 2016
The structures for liquid acetonitrile and benzonitrile were corrected to match the topology file. The virtual site particle was removed.
New liquids paperWed May 20 14:53:54 2015
A new paper by Nina Fischer and others was published "Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions", DOI:10.1021/acs.jctc.5b00190.
Virtualchemistry 2.0 is up!Fri Feb 27 14:53:54 2015
Complete overhaul of the website with lots of new data and functionality. Enjoy!
Made Caleman2012a paper availableSun Jan 15 14:53:54 2012
Uploaded the Caleman2012 paper with supporting information for download from this website, since it was published under Open Access.
New database paperThu Jan 12 09:10:41 2012
An article about this database was published in the journal Bioinformatics. The reference to the benchmark paper was updated as well.
Workaround for grompp quirkFri Jan 6 09:38:16 2012
Workaround for quirk in grompp in the order of directives in a topology file. This is about the polarizable models, where the water itp file is now included before the ions in the sample.top file.
Polarizable modelsThu Jan 5 13:57:57 2012
Added a new menu item for polarizable force fields, with at present one supported force field.
Zip files per force fieldSun Jan 1 14:59:39 2012
Zip files containing all GROMACS input files (per force field) are now available under the Molecule and Liquid DB menu item.
Updated ReferenceSun Jan 1 12:42:07 2012
Updated Caleman2012 reference in normal text and in all topology files.
Fixed error barsSun Jan 1 10:51:19 2012
Fixed error bars in simulation results to be rounded upwards in all cases.
New webserver runningFri Dec 23 16:23:40 2011
Moved the site to a new webserver, with the latest operating system, tools and disk space to grow!
Added link to GROMOS repositoryFri Dec 23 09:24:48 2011
Added link to GROMOS topology builder and repository
Fixed missing ML particleSun Dec 18 09:45:53 2011
Updated oplsaaff.itp file to contain dummy particle ML.
Benchmark paper acceptedWed Dec 7 08:17:49 2011
The benchmark paper has now been accepted officially in J. Chem. Theor. Comput. and is available online.
Added missing OPLS/AA fileWed Nov 30 07:30:54 2011
Added missing auxiliary OPLS/AA file (oplsaaff.itp) to download section for each molecule.
InChi supportMon Nov 28 14:36:05 2011
Added printing of InChi to the molecule pages.
Website nearing completionSun Nov 27 17:13:47 2011
The first version of the website is nearing completion now. Enjoy!