SPICA: Surface Property fItting Coarse grAined model

Tutoriallipid membrane

Step 3. Running simulation

Now, we have the input coordinate and it is time to prepare an input script for LAMMPS. We provide sample input scripts . Following explanation is to help understanding of the input script. There are a couple of lines user should be aware. Since SPICA exploits special form of potential function for angle and Lennard-Jones interaction, "angle_style" and "pair_style" should not be the conventional "harmonic" and "lj". LAMMPS implemented these features as the name of SDK, which is the previous version of SPICA. Thus, user should use "sdk" type for these potentials. Please refer to the following example input script and LAMMPS manual. Example input script is to equilibrate the system in NVT ensemble. In order to run the lipid membrane simulation in NPT ensemble, modify the "fix" command, such that "fix 1 all npt temp 298.15 298.15 500.0 aniso 1.0 1.0 5000.0 couple xy".

Example input script for SPICA force field:

units real
dimension 3
atom_style full
pair_style lj/sdk/coul/long 15.0 # SPICA FF employs 12-4 and 9-6 LJ functions for van der waals interaction. LAMMPS provides such pair style as SDK pair style.
pair_style lj/sdk 2.5
pair_style lj/sdk/coul/long 15.0
bond_style harmonic
angle_style hybrid sdk harmonic # To avoid angle collapse, SPICA force field assignes the LJ interaction to 1-3 interactions. As SPICA force field is fully compatible with SDK model, please use SDK angle style in LAMMPS.
angle_style sdk
angle_style hybrid sdk harmonic
dihedral_style charmm
special_bonds lj/coul 0.0 0.0 1.0
kspace_style pppm/cg 0.00001
kspace_modify order 3
kspace_modify mesh 20 20 20
# SPICA force field does not truncate the electrostatic interaction using cutoff method. In LAMMPS, use PPPM to account for the long-range interaction.
read_data system.cg.data
include system.cg.param
# Initial coordinate files prepared in the previous step.
read_data DATA.FILE
include PARM.FILE
or read_data system.cg.data
include system.cg.param
neighbor 2.0 bin
neigh_modify delay 4
timestep 5. # Based on our tests, the system is stable within the range of 5 to 10fs timestep.
minimize 1.0e-6 1.0e-5 1000 100000
fix 1 all nvt temp 298.15 298.15 100.0 drag 0.1
dump 1 all xtc 5000 dump.xtc
thermo_style multi
thermo 1000
restart 1000 system.cg.eq.rest system.cg.eq.rest
run 10000

Example input scripts:

  • Equilibration in NVT: Download
  • NPT: Download
  • To run the attached input scripts, invoke following commands:
    lmp -in in.eq -log out.eq.log
    lmp -in in.npt -log out.npt.log

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SPICA Force Field

Nagoya University