PLUMED DSEAMS_CAGES¶

The PLUMED action DSEAMS_CAGES is the seeded cage score on a group of oxygen atoms. Counts have no derivatives: they serve PRINT, COMMITTOR basins, and analysis, not biasing.

Keywords: ATOMS, CUTOFF (default 3.5 Angstrom), CANDIDATE (default 5.5), K (default 4), LENGTH_SCALE (default 10.0, PLUMED length unit to Angstrom), COMPLETE, IONS, ION_CUTOFF (default 3.5), HOPS (default 3), LIBRARY, SIGNATURE, GUESTS, GUEST_RADIUS (default 4.0).

LOAD FILE=libdseams_plumed.so
ice: DSEAMS_CAGES ATOMS=1-4096 CUTOFF=3.5 COMPLETE
PRINT ARG=ice.nice,ice.nmax,ice.nic,ice.nih,ice.chillice,ice.chillmax STRIDE=100 FILE=ICE
COMMITTOR ARG=ice.nmax STRIDE=100 BASIN_LL1=0 BASIN_UL1=20 BASIN_LL2=800 BASIN_UL2=100000
brine: DSEAMS_CAGES ATOMS=1-3000 IONS=3001-3060 ION_CUTOFF=3.5 COMPLETE
PRINT ARG=brine.nice,brine.nmax,brine.nionice,brine.nionfront,brine.nionliq STRIDE=500 FILE=BRINE
hyd: DSEAMS_CAGES ATOMS=1-2944 LIBRARY=sI_sII.keys,sI_sII_h2.keys HOPS=3
PRINT ARG=hyd.nnamed,hyd.nclasses STRIDE=500 FILE=HYDRATE
fill: DSEAMS_CAGES ATOMS=1-2944 SIGNATURE=512 GUESTS=2945-3200 GUEST_RADIUS=4.0
PRINT ARG=fill.ncages,fill.noccupied,fill.nmultiple,fill.nfreeguest STRIDE=500 FILE=FILL

That DSEAMS_CAGES block names oxygen with ATOMS. IONS stay off the graph and are read against the water assignment. LIBRARY is one topology key library from seams fingerprint --emit-library, or two or more files, comma separated, built at different hop counts; each molecule takes the deepest library that names its key. The deepest file must match HOPS. COMPLETE fills the last vertex of six-rings whose other vertices carry a label. SIGNATURE names a ring-size census (4:6,6:8) or a table entry (sodalite, alpha, 512, 51262, hc, ddc) and ncages counts the closed polyhedra that match it on the union graph. GUESTS lists one atom per guest molecule (methane carbon, THF oxygen, an ion); each guest goes to the nearest cage centre within GUEST_RADIUS, and noccupied, nmultiple and nfreeguest are the filled-cage counts a hydrate nucleation run biases and commits on.

Components include nice, nmax, nclus, nic, nih, nmixed, chillice, chillmax, chillinterfacial, sixrings, nionice, nionfront, nionliq, nclasses, and nnamed.

Source: dseams-plumed.