CGSIMRD

About

CGSIMRD, or Coarse Grained Simulation of RNA and DNA, is a software package that aids in performing coarse grain simulations of RNA and DNA using LAMMPS.

Disclaimer

This project is under active development. Stuff will break from time to time.

Dependencies

The project depends on the following software packages

• LAMMPS² (website)
• tacoxDNA¹ (website)
• oxview² (website)
• Curl² (website)

1 : cgsimrd ships with tacoxDNA.

2 : cgsimrd does not ship with LAMMPS, oxview or Curl.

Simulation Process

The simulation process has many steps. These are :

• download the necessary pdb file
• convert the pdb file into oxDNA config and topology files
• convert the oxDNA files to a LAMMPS data file
• generate an input script for LAMMPS
• perform the simulation
• convert the trajectory file into oxDNA config and topology files
• visualize the oxDNA files using oxview

Root Directory Structure

As of now, the project requires the following project structure.

.
├── inp         [ generated lammps input scripts ]
├── lib         [ tacoxDNA ]
├── lmp         [ generated lammps data files (by tacoxDNA) ]
├── pdb         [ downloaded pdb files ]
├── sim         [ generated trajectory, energy data files ]
├── oxdna_files [ store the oxdna config and topology files for visualizations ]
└── src         [ all the source scripts ]

Directories

The source directory contains the following files :

src/
 ├── cleaner.sh       --> deletes pdb or lammps data files
 ├── getpdb.sh        --> script to download pdb files
 ├── makeinput.sh     --> generates input file from template
 ├── pdb2lmp.sh       --> converts pdbs to lammps data files using tacoxDNA
 ├── setup.sh         --> creates the directories that don't 
 ├── simulate.sh      --> performs simulation using input files and lammps
 ├── tmpl_dna.in      --> template input file for DNA pdbs
 ├── tmpl_rna.in      --> template input file for RNA pdbs
 └── visualize.sh     --> visualizes trajectory file using oxview

Usage

Currently, the path to the lammps executable is set to a hardcoded path on my system. You’ll need to change that in `src/simulate.sh` to be able to run the script.