lammps/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustratedb0dec93ffb44efficient_neuronet
lammps/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated
b0dec93ffb44efficient_neuronet
frustrated
frustrated
README.TXT
README.TXT
# 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
# 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
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