Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.npt
9a0e9670fb05efficient_neuronet

Last Change
Raw File

run.in.npt
View Options

# -------- REQUIREMENTS: ---------
# 1) This example requires the CLASS2 package.
# http://lammps.sandia.gov/doc/Section_start.html#start_3
# 2) It also may require additional features and bug fixes for LAMMPS.
# So, after typing "make yes-class2" in to the shell, ...
# 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.
#
# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
# then you made a mistake in the instructions above.
#
# -- Init Section --
include system.in.init
# -- Atom Definition Section --
read_data system.data
# -- Settings Section --
include system.in.settings
# -- Run Section --
timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
dump 1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz
thermo_style custom step temp pe etotal vol epair ebond eangle
thermo 1000 # time interval for printing out "thermo" data
fix fxlan all langevin 300.0 300.0 120 48279
fix fxnph all nph x 0 0 1000 y 0 0 1000
# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon
# (for the "epsilon" used by the coarse-grained lipid), and
# to 0.33*epsilon (for the "epsilon" used in the coarse-grained protein)
# Note: The langevin damping parameter "120" corresponds to
# the 0.12ps damping time used in Watson et. al JCP 2011.
# Note: We maintain the system system at constant (zero) tention
# using a barostat damping parameter Pdamp=1000 ("0 0 1000")
# optional (not sure if this helps):
# balance x uniform y uniform
#restart 1000000
run 2000000
write_restart system_after_npt.rst
c4science · Help