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https://github.com/jbarnoud/simoji
Run a GROMACS simulation with emojis!
https://github.com/jbarnoud/simoji
emoji gromacs molecular-dynamics
Last synced: 14 days ago
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Run a GROMACS simulation with emojis!
- Host: GitHub
- URL: https://github.com/jbarnoud/simoji
- Owner: jbarnoud
- License: mit
- Created: 2017-08-06T18:32:46.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2017-08-06T21:59:07.000Z (over 7 years ago)
- Last Synced: 2024-12-24T04:41:56.111Z (16 days ago)
- Topics: emoji, gromacs, molecular-dynamics
- Language: Python
- Size: 23.4 KB
- Stars: 4
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
Simoji -- Because an emoji is better than your atom name
========================================================
Likely by accident, Gromacs has no problem using emojis where it expects
strings. This means you can use emojis as atom types, atom names, residue names
or molecule types for much more insightful simulations. Simoji replaces all
names in a topology and in a structure by emojis to run such emoji molecular
dynamics simulations.
Usage: `python3 simoji.py [options]`
Options:
* `-f`: input structure (.gro)
* `-p`: input topology (.top)
* `-t`: input correspondence table
* `-o`: output structure (.gro)
* `-op`: output topology (.top)
* `-ot`: output correspondence table
The emojis are chosen at random but coincide between the output structure and
the output topology so the files can be used together in a simulation. If the
`-ot` option is provided, simoji writes a correspondence table between the
original names and the chosen emojis. This correspondence table can be provided
as an input with the `-t` option; this bypasses the random choice of the
emojis.
If the topology file is provided with the `-p` option, and if it includes ITP
files, the translated content of these ITP file is concatenated in the
resulting topology.
As an example, here is a extract of the POPC topology in the Martini coarse
grained force field [1]:
```
[moleculetype]
; molname nrexcl
POPC 1
[atoms]
; id type resnr residu atom cgnr charge
1 Q0 1 POPC NC3 1 1.0
2 Qa 1 POPC PO4 2 -1.0
3 Na 1 POPC GL1 3 0
4 Na 1 POPC GL2 4 0
5 C1 1 POPC C1A 5 0
6 C1 1 POPC C2A 6 0
7 C3 1 POPC D3A 7 0
8 C1 1 POPC C4A 8 0
9 C1 1 POPC C1B 9 0
10 C1 1 POPC C2B 10 0
11 C1 1 POPC C3B 11 0
12 C1 1 POPC C4B 12 0
```
Here is the same fraction emojified:
```
[moleculetype]
; molname nrexcl
⚛ 1
[atoms]
; id type resnr residu atom cgnr charge
1 ⛽ 1 ⚛ 🍲 1 1.0
2 📝 1 ⚛ 🌭 2 -1.0
3 🐍 1 ⚛ 🍹 3 0
4 🐍 1 ⚛ 🤐 4 0
5 🕷 1 ⚛ 🕓 5 0
6 🕷 1 ⚛ 🚊 6 0
7 🚕 1 ⚛ 🚓 7 0
8 🕷 1 ⚛ 🔇 8 0
9 🕷 1 ⚛ 🕝 9 0
10 🕷 1 ⚛ 🗨 10 0
11 🕷 1 ⚛ 🎑 11 0
12 🕷 1 ⚛ 👂 12 0
```
Note that simoji requires python 3. It will not work on python 2.
You should probably not use emojis in your serious simulations 😝.
[1] The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
Siewert J. Marrink, H. Jelger Risselada, Serge Yefimov, D. Peter Tieleman, and, and Alex H. de Vries
The Journal of Physical Chemistry B 2007 111 (27), 7812-7824
DOI: http://dx.doi.org/10.1021/jp071097f