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 here. 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, the previous version of SPICA. In LAMMPS patch 3 AUG 2022, the package SDK was renamed to SPICA. So, the style name sdk was also renamed to spica, though the old one is still available for backword compatibility.
Please refer to the following LAMMPS manual.

• CG-SPICA package
• angle_style spica
• pair_style lj/spica

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.
Check the following example input script.

Example input script (in.eq) for SPICA force field:

units real dimension 3 atom_style full newton on off read_data DATA.FILE include PARM.FILE kspace_style pppm/cg 0.00001 kspace_modify order 3 kspace_modify mesh 20 20 20

neighbor 2.0 bin neigh_modify delay 4

timestep 10 minimize 1.0e-6 1.0e-5 1000 10000 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 10000 eq.rest eq.rest run 20000

Example input scripts:

• Equilibration in NVT: in.eq
• NPT: in.npt
• 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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