ZnTrack enabled MDAnalysis Toolkits with full parameter and result tracking capabilities.
import znmdakit
project = znmdakit.Project()
with project:
system = ips.Smiles2Gromacs(
smiles=[BMIM, BF4],
density=0.5,
count=[64, 64],
labels=["Im", "BF"],
config_files=mdp_files,
fudgeLJ=1,
fudgeQQ=1,
itp_files=itps,
pdb_files=pdbs,
tolerance=1.8,
cleanup=True,
maxwarn=0,
)
universe = znmdakit.Universe(
# data_file=znflow.resolve(system.traj_file), # hotfix for https://github.com/zincware/ZnTrack/pull/875
data=system.frames, # can be either one
residues={"BF": BF4, "Im": BMIM},
)
with project.group("BF4"):
znmdakit.InterRDF(
universe=universe.universe,
g1="name COM and resname BF", # replace with e.g. name O and set apply_com_transform=False
g2="name COM and resname BF",
nbins=1000,
apply_com_transform=True,
)
msd = znmdakit.EinsteinMSD(
universe=universe.universe,
select="name COM and resname BF",
timestep=0.001, # ps
sampling_rate=1000, # ps
apply_com_transform=True,
)
znmdakit.SelfDiffusionFromMSD(
data=msd,
start_time=2000,
end_time=7000,
always_changed=False,
)
project.build()znmdakit.RDFznmdakit.EinsteinMSD