Table 1. Size in atoms, length of productions MD simulations, temperature, speed of the simulations on Frontera at TACC and lipid composition of the flat bilayers and the vesicle of the different systems.
qscff | 1699436 atoms | 750 ns | 310 K | 24 ns/day with 16 nodes | |||||
Upper bilayer | CHL1 | POPC | POPS | SAPE | SDPE | SDPS | total | ||
Upper leaflet | 540 | 468 | 0 | 72 | 120 | 0 | 1200 | ||
% | 45 | 39 | 0 | 6 | 10 | 0 | |||
Lower leaflet | 540 | 146 | 84 | 120 | 240 | 96 | 1226 | ||
% | 44 | 11.9 | 6.9 | 9.8 | 19.6 | 7.8 | |||
Lower bilayer | CHL1 | POPC | POPS | SAPI2D | SAPE | SDPE | SDPS | total | |
Upper leaflet | 540 | 134 | 120 | 60 | 84 | 168 | 120 | 1226 | |
% | 44 | 11 | 9.8 | 4.9 | 6.9 | 13.7 | 9.8 | ||
Lower leaflet | 540 | 538 | 0 | 0 | 48 | 84 | 0 | 1200 | |
% | 45 | 44 | 0 | 0 | 4 | 7 | 0 | ||
sqscff | 1700475 atoms | 270 ns | 310 K 24 ns/day with 16 nodes | ||||||
qscv | 3222393 atoms | 520 ns | 310 K | 23 ns/day with 32 nodes | |||||
454 ns | 325 K | ||||||||
Vesicle | CHL1 | POPC | SAGL | SAPE | SAPI2D | SDPE | SDPS | SOPS | total |
Outer leaflet | 1258 | 296 | 0 | 534 | 0 | 282 | 210 | 199 | 2779 |
% | 45.3 | 10.6 | 0 | 19.2 | 0 | 10.1 | 7.6 | 7.2 | |
Inner leaflet | 814 | 668 | 0 | 183 | 0 | 99 | 1 | 1 | 1766 |
% | 46.1 | 37.8 | 0 | 10.4 | 0 | 5.6 | 0.1 | 0.1 | |
Flat bilayer | CHL1 | POPC | SAGL | SAPE | SAPI2D | SDPE | SDPS | SOPS | total |
Upper leaflet | 540 | 96 | 12 | 84 | 60 | 156 | 120 | 120 | 1188 |
% | 45.4 | 8.1 | 1 | 7.1 | 5.1 | 13.1 | 10.1 | 10.1 | |
Lower leaflet | 540 | 516 | 12 | 36 | 0 | 84 | 0 | 0 | 1188 |
% | 45.4 | 43.4 | 1 | 3 | 0 | 7.1 | 0 | 0 | |
prsg | 5056443 atoms | 336 ns | 310 K | 13 ns/day with 32 nodes | |||||
Flat bilayer | CHL1 | POPC | SAGL | SAPE | SAPI2D | SDPE | SDPS | SOPS | total |
Upper leaflet | 830 | 151 | 18 | 132 | 93 | 262 | 182 | 181 | 1849 |
% | 44.9 | 8.2 | 1 | 7.1 | 5 | 14.2 | 9.8 | 9.8 | |
Lower leaflet | 810 | 774 | 18 | 72 | 0 | 126 | 0 | 0 | 1800 |
% | 45 | 43 | 1 | 4 | 0 | 7 | 0 | 0 | |
prs2 | 5870280 atoms | 310 ns | 310 K | 16 ns/day 48 nodes | |||||
Flat bilayer | CHL1 | POPC | SAGL | SAPE | SAPI2D | SDPE | SDPS | SOPS | total |
Upper leaflet | 1035 | 184 | 23 | 161 | 115 | 322 | 230 | 230 | 2300 |
% | 45 | 8 | 1 | 7 | 5 | 14 | 10 | 10 | |
Lower leaflet | 1009 | 964 | 22 | 88 | 0 | 154 | 0 | 0 | 2237 |
% | 45.1 | 43.1 | 1 | 3.9 | 0 | 6.9 | 0 | 0 | |
prsncpxca | 5870246 atoms | 439 ns | 310 K | 16 ns/day 48 nodes |
Vesicle: same as qscv system.
Flat bilayer: same as prs2 system.