Centered gas-phase structures

Mon 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 files

Thu 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 structures

Mon 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 paper

Wed 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 available

Sun 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 paper

Thu 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 quirk

Fri 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 file.

Polarizable models

Thu 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 field

Sun 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 Reference

Sun Jan 1 12:42:07 2012

Updated Caleman2012 reference in normal text and in all topology files.

Fixed error bars

Sun Jan 1 10:51:19 2012

Fixed error bars in simulation results to be rounded upwards in all cases.

New webserver running

Fri 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 repository

Fri Dec 23 09:24:48 2011

Added link to GROMOS topology builder and repository

Fixed missing ML particle

Sun Dec 18 09:45:53 2011

Updated oplsaaff.itp file to contain dummy particle ML.

Benchmark paper accepted

Wed 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 file

Wed Nov 30 07:30:54 2011

Added missing auxiliary OPLS/AA file (oplsaaff.itp) to download section for each molecule.

InChi support

Mon Nov 28 14:36:05 2011

Added printing of InChi to the molecule pages.

Website nearing completion

Sun Nov 27 17:13:47 2011

The first version of the website is nearing completion now. Enjoy!