Coarse-grained molecular model of DNA (for LAMMPS)
The USER-3SPN2 directory contains the source code needed to run simulations of the 3SPN.2 coarse-grained DNA model within the LAMMPS MD package. 3SPN.2 is a highly-robust coarse-grained DNA model that is capable of studying processes such as hybridization and DNA protein interactions. For details about the model itself and it's development, please see Hinckley et al., JCP, 139, 144903 ,2013 (DOI: 10.1063/1.4822042)
The directory also contains sample input files for a normal simulation of a DNA duplex, a restart, and a parallel tempering calculation.
Also include is a directory containing a configuration generator that generates B-DNA according to the crystal structure of Arnott et al. This configuration generator will generate data files that can be read in as data files using the sample .in files.
Also include is a .pdf containing additional documentation and instructions for compiling and visualization.
If you have any questions and concerns associated with bugs (not with general (non-3SPN.2) compilation or LAMMPS issuyes!) please direct your inquiries to Dan Hinckley (hinckley.dan@gmail.com).
The following website has historically held information regarding on-going improvements to the 3SPN.2 model, as well as recent publications by the de Pablo group and others.
http://ime.uchicago.edu/de_pablo_lab/research/dna_folding_and_hybridization/3spn.2/
Moving forward, we hope to coordinate all updates and communication through github.
USER-3SPN has not been tested with versions of LAMMPS newer than 13 Jan 2014. We welcome pull requests that update USER-3SPN2 to be compatable with more recent versions of LAMMPS. In the meantime however, it is recommended that you use the 13 Jan 2014 version of LAMMPS for your simulations.
The GCGI/ directory was added, which contains necessary files for using the general coarse- grained ions model presented by Hinckley and de Pablo, JCTC (2015) (DOI:10.1021/acs.jctc.5b00341).