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) |
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.