# This directory demonstrates how to run a short simulation of
# the "frustrated" coarse-grained protein model used in:
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
# (http://www.pnas.org/content/101/36/13192)
#
# During this short simulation (run_short_sim.nvt.in) the protein evolves
# from an unfolded initial conformation to a misfolded conformation.
# (Visualize using VMD. Note: It can take hundreds of millions of
# timesteps to escape from this conformation and reach the folded state.)
#
# -------- REQUIREMENTS: ---------
# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
# http://lammps.sandia.gov/doc/Section_start.html#start_3
# 2) It also may require additional features and bug fixes for LAMMPS.
# be sure to download and copy the "additional_lammps_code" from
# http://moltemplate.org (upper-left corner menu)
# 3) Unpack it
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
# 5) Compile LAMMPS.

-------------
Instructions on how to build LAMMPS input files and
run a short simulation are provided in other README files.

step 1)
README_setup.sh

step2)
README_run.sh