The GMX-Plugin [jar]
Posted: 12.01.2015, 08:59
The GMX-Plugin
The GMX-Plugin is an interface between GROMACS 4.X and the MembraneEditor 2.2.2.
It uses the force field ffGMX45a3 and special lipid topologies which can also be downloaded here.
Learn here how to import this algorithm into the WebStart or Standalone version:
http://cellmicrocosmos.org/index.php/cm ... algorithms
The GMX-Plugin
Developers: Sebastian Rubert, Christian Gamroth
Important: There is a small bug in the actual MembraneEditor version 2.2.2_1! If you are using the GMX-Plugin, please make sure that you activate in the PDB Output Settings "Write additional APL@Voro config file". Otherwise the topology file will not be correctly written. In future versions, this bug will be fixed!
Features
The plugin was used for the conference paper:
http://ceur-ws.org/Vol-826/paper05.pdf
The United Atom Lipid Library
Developers: André Heissmann, Ralf Rotzoll
This library contains the following lipids based on ffG45a3:
http://cellmicrocosmos.org/index.php/cm ... your-files
The Coarse-Grained Lipid Library
Developers: Gunther Lukat, Alexander Schäfer
Please see the README.txt file for further instructions or
http://cellmicrocosmos.org/index.php/cm ... your-files
For more information about MARTINI, please visit:
http://md.chem.rug.nl/cgmartini/
This library contains the following lipids:
Project Leaders: Björn Sommer, Jens Krüger
The GMX-Plugin is an interface between GROMACS 4.X and the MembraneEditor 2.2.2.
It uses the force field ffGMX45a3 and special lipid topologies which can also be downloaded here.
Learn here how to import this algorithm into the WebStart or Standalone version:
http://cellmicrocosmos.org/index.php/cm ... algorithms
The GMX-Plugin
Developers: Sebastian Rubert, Christian Gamroth
Important: There is a small bug in the actual MembraneEditor version 2.2.2_1! If you are using the GMX-Plugin, please make sure that you activate in the PDB Output Settings "Write additional APL@Voro config file". Otherwise the topology file will not be correctly written. In future versions, this bug will be fixed!Features
- Standard Workflow for GROMACS (editconf/minimize/equilibrate/MD simulation)
- Edit Workflow
- Connect via SSH to external server and start GROMACS jobs
- Local GROMACS support
- Automatic building of PDB file based on the MembraneEditor membrane
- Automatic definition of the topology file and the box size
- Based on ffG45a3
- Interactive GROMACS commands
- GROMACS 5 commands
The plugin was used for the conference paper:
http://ceur-ws.org/Vol-826/paper05.pdf
The United Atom Lipid Library
Developers: André Heissmann, Ralf Rotzoll
This library contains the following lipids based on ffG45a3:
- CDN
- CHO
- DPC
- DPE
- DPS
- PIB
- POC
- PPS
http://cellmicrocosmos.org/index.php/cm ... your-files
The Coarse-Grained Lipid Library
Developers: Gunther Lukat, Alexander Schäfer
Please see the README.txt file for further instructions or
http://cellmicrocosmos.org/index.php/cm ... your-files
For more information about MARTINI, please visit:
http://md.chem.rug.nl/cgmartini/
This library contains the following lipids:
- DOPC
- DOPE
- DOPI
- DPPI
- DPPI
- DPPS
- DUPC
- and more ...
Project Leaders: Björn Sommer, Jens Krüger