This new sub-forum contains a set of algorithms to be used in conjunction with the MembraneEditor. [jar] files can be used with the standalone and the web start edition, [java] files can only be used with the standalone edition, but contain the source code. For more information on plugin development, please see: http://cellmicrocosmos.org/index.php/developer
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bjoern
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The GMX-Plugin [jar]

Post by bjoern » 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
GROMACS_Plugin_build09012015.jar
The GMX-Plugin build 09.01.2015
(496.77 KiB) Downloaded 950 times
:!: 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
Not supported yet
  • Interactive GROMACS commands
  • GROMACS 5 commands
Please use the lipid library below to generate membranes.

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
GMX-Plugin-Lipids.zip
The lipid library for the GMX-Plugin containing also the file lipidsFFG45a3.itp
(24.19 KiB) Downloaded 904 times
This library contains the following lipids based on ffG45a3:
  • CDN
  • CHO
  • DPC
  • DPE
  • DPS
  • PIB
  • POC
  • PPS
Please copy the lipids into the directory /Cm2_Workspace/Pdb_Files and then just import the files into the database of the MembraneEditor as described here:
http://cellmicrocosmos.org/index.php/cm ... your-files


The Coarse-Grained Lipid Library

Developers: Gunther Lukat, Alexander Schäfer
GMX-Plugin-CG-Lipids.zip
The coarse-grained lipid library for the GMX-Plugin for the MARTINI force field
(54.89 KiB) Downloaded 910 times
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

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