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. 2024 May 8;20(10):4325–4337. doi: 10.1021/acs.jctc.3c01333

Table 1. Systems Simulated Specifically for This Worka.

lipid:salt force field ion (M) Nl Nw Nc T (K) ts (ns) ta (ns) teq files [ref]
POPC Drude2017 0 144 6400 0 303 500 400 5.79 (81)
  Drude2023 0 72 2239 0 303 300 200 2.29 ± 0.13 (82, 60)
POPE Drude2017 0 144 6400 0 308 350 300 5.79 (83)
  Drude2023 0 72 2304 0 303 300 200 1.71 ± 0.10 (59, 84)
  AMOEBA 0 72 2880 0 303 306 306 0.43 (85)
POPC:NaCl Drude2017 0.350 144 6400 41 303 500 400 3.31 (86)
  Drude2017 0.450 144 6400 51 303 500 400 2.5 (87)
  Drude2017 0.650 144 6400 77 303 500 400 3.30 (88)
  Drude2017 1.0 144 6400 115 303 500 400 4.06 (89)
  Drude2023 0.350 128 6400 41 303 224 220 2.63 (90)
  Drude2023 1.0 128 6400 115 303 220 220 2.77 (91)
POPC:CaCl2 Drude2017 0.350 144 6400 41 303 500 400 2.45 (92)
  Drude2017 0.450 144 6400 52 303 500 400 2.56 (93)
  Drude2017 0.650 144 6400 76 303 500 400 4.46 (94)
  Drude2017 1.0 144 6400 114 303 500 400 5.00 (95)
  Drude2023 0.350 128 6400 41 303 219 219 2.63 (96)
  Drude2023 0.790 128 6400 91 303 214 214 4.32 (97)
DOPC AMOEBA 0 72 2880 0 303 202 202 0.62 (98)
DOPC:NaCl AMOEBA 0.450 72 2880 17 303 218 218 0.60 (99)
  AMOEBA 1.0 72 2880 35 303 202 202 0.61 (100)
DOPC:CaCl2 AMOEBA 0.450 72 2880 16 303 218 218 0.53 (101)
  AMOEBA 1.0 72 2880 36 303 218 218 0.66 (102)
a

Column Nl gives the number of lipids, Nw the number of water molecules, and T (K) denotes the temperature in kelvins. The salt concentrations in column “ion (M)” is calculated from the number of cations Nc as [salt] = Nc × [water]/Nw, where [water] = 55.5 M. Simulated time is listed in column ts and time used for analysis in ta. Column teq gives the relative equilibration times with respect to the trajectory lengths based on PCAlipids76,77 and computed using the NMRlipids Databank:40teq < 1 indicates convergence, teq > 1 indicates the presence of a longer time-scale than the trajectory length. Column “files [ref]” gives the reference to openly accessible simulation data.