All files provided below are in compressed (tgz and tar.gz) format. They can be opened using decompression software such as WinRAR or 7-zip or, if you are a Unix/Linux terminal user, with "tar xvf".
Force Field ParametersThe following links contain all force field files required to run simulations with systems produced by GNOMM:
Configuration FilesHere you will find example configuration files (*.mdp) to prepare and run simulations with GROMACS version 5.0 or newer:
PACE is a hybrid force field, combining a United-Atom representation for the proteins with the MARTINI Coarse-Grained force field for lipids and the solvent. This means that in addition to the standard potential energy function, a number of additional potentials are defined to model multiscaling, namely, a set of extra potentials for the phi/psi dihedral angles of the backbone, an additional function to model directionality in polar interactions and hydrogen bonds and a special, hybrid Lennard-Jones term to model non-bonded interactions between atomic and Coarse-Grained particles. These require special modifications to the GROMACS source to be operable. For this reason, compilation of tpr files with grompp requires a specially modified version of GROMACS v. 3.3.1.
Note that modified GROMACS 3.3.1 is required *only* for the generation of tpr files with grompp. The actual simulations can be performed with any newer version of GROMACS, including versions 4.x, 5.x, 2016.x and 2018.1.
PACE for GROMACS can be obtained either from the TCBG group or by Wei Han's new lab website.
Instructions on compiling the code and using it with PACE are given with the source code.
Fotis A. Baltoumas, Stavros J. Hamodrakas & Vassiliki A. Iconomidou (2019)
The Gram-Negative Outer Membrane Modeler: automated building of lipopolysaccharide-rich bacterial outer membranes in four force fields
J. Comput. Chem. Jul 5; 40(18): 1727-1734, DOI: 10.1002/jcc.25823