Update repo

data/lnp_empty_310/CPP1.86_9.41_3.0/inp.yml

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+comment: "3-bead Cooke lipid model. For more information: doi:10/chqzjk"
+temperature: 310
+random: {seed: hardware}
+geometry: {type: hexagonal, length: 87.96459430051421, radius: 32.406022233435095}
+mcloop: {macro: 10, micro: 200000.0}
+
+atomlist:
+    - HD:  {sigma: 5.000000000000002, eps: 2.5774950000000003, dp: 2}
+    - HHD: {sigma: 5.000000000000002, eps: 2.5774950000000003, dp: 2, q: 1}
+    - T1:  {sigma: 6.499999999999998, eps: 2.5774950000000003, dp: 2}
+    - T2:  {sigma: 8.499999999999998, eps: 2.5774950000000003, dp: 2, alphax: -18}
+    - NA:  {sigma: 4.6, eps: 0.01, dp: 10, q: 1}
+    - CL:  {sigma: 4.6, eps: 0.01, dp: 10, q: -1}
+    - H:   {pactivity: 3.0, eps: 0.01, implicit: True}
+
+moleculelist:
+    - Na: {atoms: [NA], atomic: True, activity: 0.1183475840494453}
+    - Cl: {atoms: [CL], atomic: True, activity: 0.11816982211691233}
+    - lipid:
+        activity: 3.890449936382145e-10
+        structure:
+            - HD: [0,0,0]
+            - T1: [0,0,5.75]
+            - T2: [0,0,13.25]
+        bondlist:
+            - fene: {index: [0,1], k: 1.2, rmax: 8.625}
+            - fene: {index: [1,2], k: 1.2, rmax: 11.249999999999996}
+            - harmonic: {index: [0,2], k: 0.4, req: 26.624999999999996}
+        keeppos: True
+
+insertmolecules:
+    - Na: {N: 400, inactive: True}
+    - Cl: {N: 400, inactive: True}
+    - lipid: {N: 400, inactive: True}
+
+energy:
+    - bonded: {}
+    - nonbonded_splined:
+        default:
+            - wca:
+                mixing: LB
+            - custom:
+                cutoff: 1000
+                function: lB * q1 * q2 * ( 1.0 / r - 1.0 / Rc )
+                constants:
+                    lB: 10.898630255420876
+            - polar: {epsr: 74.18851892903221}
+        T1 T1:
+            - wca:
+                mixing: LB
+            - cos2: {rc: 7.296002999999999, eps: 2.5774950000000003, wc: 11.699999999999998}
+        T1 T2:
+            - wca:
+                mixing: LB
+            - cos2: {rc: 8.418465, eps: 2.5774950000000003, wc: 13.499999999999996}
+        T2 T2:
+            - wca:
+                mixing: LB
+            - cos2: {rc: 9.540926999999998, eps: 2.5774950000000003, wc: 15.299999999999997}
+
+reactionlist:
+    - "HHD = HD + Na + H": {pK: 9.41}
+    - "HHD + Cl = HD + H": {pK: 9.41}
+    - "= Na + Cl": {}
+    - "= lipid": {neutral: True}
+
+moves:
+    - rcmc: {repeat: 20}
+    - moltransrot: {molecule: lipid, dp: 0.2, dprot: 0.5, repeat: 200}
+    - transrot: {molecule: lipid, repeat: 10}
+    - transrot: {molecule: Cl, repeat: N}
+    - transrot: {molecule: Na, repeat: 10}
+    - volume: {dV: 0.05, method: isochoric, repeat: 1}
+
+analysis:
+    - savestate: {file: state.json}
+    - savestate: {file: confout.pqr}
+    - savestate: {file: confout.gro}
+    - xtcfile: {file: traj.xtc, nstep: 1e4}
+    - systemenergy: {file: energy.dat, nstep: 1e4}
+    - savestate: {file: cuboid.pqr, convert_hexagon: True, nstep: 1e6}
+    - qrfile: {file: qrtraj.dat, nstep: 1e4}
+    - reactioncoordinate: {file: charge.dat, nstep: 1e3, type: system, property: Q}
+    - reactioncoordinate: {file: order.dat, nstep: 1e3, type: system, property: OrderParam, index: 2}
+    - reactioncoordinate: {file: NNa.dat, nstep: 1e3, type: molecule, property: N, index: 0}
+    - reactioncoordinate: {file: NCl.dat, nstep: 1e3, type: molecule, property: N, index: 1}
+    - reactioncoordinate: {file: Nlipids.dat, nstep: 1e3, type: atom, property: N, index: 2}
+    - reactioncoordinate: {file: radius.dat, nstep: 1e3, type: system, property: radius}
+    - reactioncoordinate: {file: Lz.dat, nstep: 1e3, type: system, property: Lz}
+    - reactioncoordinate: {file: NHHD.dat, nstep: 1e3, type: atom, property: N, index: 1}
+    - reactioncoordinate: {file: RCl.dat, nstep: 1e3, type: molecule, property: Rinner, indexes: [2,3,5,5], dir: [1,1,0]}
+    - reactioncoordinate: {file: Rcyl.dat, nstep: 1e3, type: molecule, property: Rinner, indexes: [2,3,0,1], dir: [1,1,0]}
+    - atomprofile: {file: distCL.dat, nstep: 1e3, atoms: [CL], dir: [1,1,0], atomcom: T1, dr: 0.2}