https://github.com/bio-phys/cnt-martini
Generates Martini models for open carbon nanotubes to use with Gromacs.
https://github.com/bio-phys/cnt-martini
Last synced: 5 months ago
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Generates Martini models for open carbon nanotubes to use with Gromacs.
- Host: GitHub
- URL: https://github.com/bio-phys/cnt-martini
- Owner: bio-phys
- License: mit
- Created: 2018-02-02T13:26:05.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2021-11-24T01:39:12.000Z (over 4 years ago)
- Last Synced: 2025-09-09T19:36:19.758Z (9 months ago)
- Language: Python
- Size: 105 KB
- Stars: 15
- Watchers: 4
- Forks: 4
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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] \
-bf [bond force const.] \
-af [angle force const.] \
-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] \
--base36
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.
## Notes
* By default, atom names are a letter denoting their function (C - plain carbon grid, F - funcional group) plus the last three digits of their atom number (decimal system). The flag `--base36` switches to a base of 36 (including letters) to expand the number of unique atom names from 10^3 = 1000 (decimal) to 36^3 = 46656.
* For large CNTs, a higher force constant than the standard value of 5000 should be used. A rule of thumb is to use a value of 20000 if the circumference exceeds 10 beads/ring or the length exceeds 15 rings.
* The script produces position restraints, too. These are usually inteded for equilibration. They will not work with a Parrinello-Rahman barostat.
## 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).