MD parameters

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These are some example of a general input parameter files for molecular dynamics simulations with . For further background reading on comparison of the different .mdp options, plese 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

Martini 3

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• martini_v3.x_example.mdp

Martini 2

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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.

• martini_v2.x_new-rf.mdp

• martini_v2.x_new.mdp

• martini_v2.x_forcemod.mdp

• martini_v2.x_common.mdp

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.

• martini_v2.x_example.mdp

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

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