Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/run.in.nvt
12150ffa7397lammm-devel

Last Change
Raw File

run.in.nvt
View Options

# -------- 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.
# So, after typing "make yes-user-misc" 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.
# 6) Minimize the system using:
# lmp_mpi -i run.in.npt
# (assuming "lmp_mpi" is the name of the lammps binary you created in step 5)
#
# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
# then you made a mistake in the instructions above.
#
# ------------------------------- Initialization Section --------------------
include system.in.init
# ------------------------------- Atom Definition Section -------------------
# Commenting out:
#
# read_data system.data
#
# Instead read the data file created by "run.in.min".
read_data system_after_min.data
# ------------------------------- Settings Section --------------------------
include system.in.settings
# ------------------------------- Run Section -------------------------------
# Just in case the previous minimization failed, try again.
# (I don't know why this helps, but sometimes it does. Magic.)
minimize 1.0e-5 1.0e-7 5000 20000
# Run main simulation
timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
dump 1 all custom 2500 traj_nvt.lammpstrj id mol type x y z ix iy iz
thermo_style custom step temp pe etotal vol epair ebond eangle
thermo 100 # time interval for printing out "thermo" data
fix fxlan all langevin 300.0 300.0 120 48279
fix fxnve all nve
# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB.
# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon.
# Note: The langevin damping parameter "120" corresponds to
# the 0.12ps damping time used in Watson et. al JCP 2011.
run 1000000
write_data system_after_nvt.data
c4science · Help