- Last Updated: Thursday, 09 February 2017 00:48
Example of a general input parameter files for Gromacs 5. For comparison of the different .mdp options see:
- D.H. de Jong, S. Baoukina, H.I. Ingólfsson, Marrink S.J. Martini straight: boosting performance using a shorter cutoff and GPUs. Comput. Phys. Commun., 199:1-7, 2016. doi:10.1016/j.cpc.2015.09.014
Based on the extensive testing, we recommend the new-rf.mdp parameters for most cases. However not all systems have been tested and we recommend you do your own tests. In addition, for consistency within a project the same .mdp options should always be used.
Example of a general input parameter files (Gromacs 4). Explanations on the various options and which options to change for the use with polarizable water are given inside the file.Older mdp-files (gromacs 3) for reference purpose only. Version 2.x. is for version 2.0, 2.1 and 2.2, 2.P is for use with polarizable water (2.P and 2.2P). martini_v2.x_example.mdp martini_v2.P_example.mdp