cnt-martini's Introduction

Open Carbon Nanotubes for the Martini Model

Generates a Martini model for an open carbon nanotube (CNT) for use with the Gromacs simulation package. It provides a structure file (.gro), a topology-include file (.itp) and a position-restraints file (.itp).

Tools to analyze Martini CNT simulations can be found here: https://github.com/bio-phys/cnt-martini-analysis.

Requirements

Python (2/3) with packages argparse, math, and sys

Usage

For a new nanotube model, run

python martini-cnt-generator.py -nr [number of rings] -rs [number of beads per ring] -bl [bond length] -bt [bead type] -ft [bead type of the functional groups] -fb [number of functionalized rings at one end] -fe [number of functionalized rings at the other end]

for example

python martini-cnt-generator.py -nr 12 -rs 8 -bl 0.47 -bt CNP -ft SNda -fb 1 -fe 1

All arguments are optional. If an argument is not used, the default value for the standard CNT porin [1] is used.

Literature

If the script or the model is helpful, please cite:

[1] M. Vögele, J. Köfinger, G. Hummer: Simulations of Carbon Nanotube Porins in Lipid Bilayers. Faraday Discuss., 2018, 209, 341-358, DOI: 10.1039/C8FD00011E
http://pubs.rsc.org/en/content/articlelanding/2018/fd/c8fd00011e

The model is based on previous work:

[2] R. M. Bhaskara, S. M. Linker, M. Vögele, J. Köfinger, G. Hummer Carbon Nanotubes Mediate Fusion of Lipid Vesicles. ACS Nano, 2017, 11 (2), pp 1273–1280
[3] M. Vögele, G. Hummer: Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes. J. Phys. Chem. B, 2016, 120 (33), pp 8722–8732 DOI: 10.1021/acs.jpcb.6b05102
[4] S. Baoukina, L. Monticelli, D.P. Tieleman: Interaction of Pristine and Functionalized Carbon Nanotubes with Lipid Membranes. J. Phys. Chem. B (2013), 117, 12113-23.
[5] L. Monticelli On atomistic and coarse-grained models for C60 fullerene. J. Chem. Theory Comput. (2012), 8, 1370−1378 (DOI: 10.1021/ct3000102).

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