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Renamed force field files

The GAFF force field files for liquid topologies based on the Caleman2012 paper and the Fischer2015 paper have been renamed in order to prevent confusion, to GAFF-ESP-2012.zip respectively GAFF-ESP-2012-Amber.zip. The ESP denomination is to signify that the ESP method was used to derive charges.

Alexandria

Thi Nov 15 13:19:43 CET 2018

A new section on the website has been added about the Alexandria project our work towards a new force field.

Paper on gas-phase properties

Fri Oct 26 11:49:13 CET 2018

A new paper on gas-phase properties of simulated compounds was published and the results and input files will be distributed here. Force fields used were GAFF, with both ESP and BCC charges, and CGenFF for about 1800 compounds. The paper, entitled "Small Molecule Thermochemistry: A Tool for Empirical Force Field Development" can be found here.

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 sample.top 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.

StdInChi support

Mon Nov 28 14:36:05 2011

Added printing of StdInChi 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!


Home Alexandria News Compound database Properties studied Force field packages Correlation tool F.A.Q. Links People Funding Contact	News Renamed force field files The GAFF force field files for liquid topologies based on the Caleman2012 paper and the Fischer2015 paper have been renamed in order to prevent confusion, to GAFF-ESP-2012.zip respectively GAFF-ESP-2012-Amber.zip. The ESP denomination is to signify that the ESP method was used to derive charges. Alexandria Thi Nov 15 13:19:43 CET 2018 A new section on the website has been added about the Alexandria project our work towards a new force field. Paper on gas-phase properties Fri Oct 26 11:49:13 CET 2018 A new paper on gas-phase properties of simulated compounds was published and the results and input files will be distributed here. Force fields used were GAFF, with both ESP and BCC charges, and CGenFF for about 1800 compounds. The paper, entitled "Small Molecule Thermochemistry: A Tool for Empirical Force Field Development" can be found here. 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 sample.top 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. StdInChi support Mon Nov 28 14:36:05 2011 Added printing of StdInChi 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!