*** Welcome to our DMB data repository!*** 
 
Here are results from the simulations of two DNA mini-dumbbell sequences
tested with a variety of currently available force fields.
       	   "TTTA" d(TTTA-TTTA)
	   "CTTG" d(CTTG-CATG)

The publication describing this work is:

Winkler, L.; Galindo-Murillo, R.; Cheatham, T. E. I. Structures and Dynamics of
DNA Mini-Dumbbells Are Force Field Dependent. J. Chem. Theory Comput. 2023.
https://doi.org/10.1021/acs.jctc.3c00130.


In this directory are trajectories and topologies processed via CPPTRAJ.
CPPTRAJ is part of AmberTools and is available at http://www.ambermd.org.
Simulations were performed for five independent replicas for 5 microseconds
per replica. Trajectories provided here are the aggregated, solvent/ion
stripped trajectories. Simulations were typically run with the OPC water model
unless otherwise noted in the manuscript.

Naming for the files in the directory is as follows:
       - The first four letters of the files are the first for letters of the
       	 DNA sequence it corresponds to. (TTTA= d(TTTA-TTTA))
       - The next few letters corresponds to the force field used to run the
       	 simulations. (Charmm36=C36)
       - .nc files are trajectories while .topo files are topology files


       For more details, e-mail: tec3@utah.edu