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,
should not be the conventional harmonic
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
Please refer to the following 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
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:
newton on off
kspace_style pppm/cg 0.00001
kspace_modify order 3
kspace_modify mesh 20 20 20
neighbor 2.0 bin
neigh_modify delay 4
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
restart 10000 eq.rest eq.rest
Example input scripts: