The dimerizer script for Dimer simulations in Gromacs
Project description
# dimerizer — This is a tool to convert a standard Gromacs input to a dimerized one. [Gromacs](http://www.gromacs.org/) is a popular tool for proteins simulation. This script allows to run Gromacs simulations with [Dimer Metadynamics](http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00691), a replica exchange method recently introduced to enhance the sampling of a probability distribution. This scripts takes a standard Gromacs input, that consists of: * A simulation settings file (.mdp) * An initial configuration file (.pdb) * A topology file (.top) * A forcefield folder, here we have tested charmm22* and charmm36 but any charmm forcefield should work.
The result are modified files for the dimer replicas. See the examples folder for a quickstart, and the doc folder for the inner workings of the script. A paper will be shortly published to explain in details how this is done and show some benchmark and new tests of Dimer Metadynamics.
This is a python2.7 code, to install it remember to use the correct pip version (i.e. pip2.7).
# Auxiliary scripts
There are also two support scripts that help setting up and controlling the simulation.
## plread
plread scans through plumed.*.dat files in search for the keyword given as argument and then allows to edit the value in each of the file with a single command.
## tune_replicas
tune_replicas is a script that given the parameters of the first replica will create a number of replicas with parameters so that the exchange probabilities are close to the target value.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
File details
Details for the file dimerizer-1.0.1.tar.gz
.
File metadata
- Download URL: dimerizer-1.0.1.tar.gz
- Upload date:
- Size: 2.5 MB
- Tags: Source
- Uploaded using Trusted Publishing? No
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 |
d23c7413958cc5c4a7e0d6a38c74774e00e499a368608a1ee58ca9035652cf30
|
|
MD5 |
32b270bb69d2287f9c7200c462e68458
|
|
BLAKE2b-256 |
2433d11ad6744192b805933519e413ddf24d7ca8e28e29e624daf04bbd28d676
|