;;;;; Martini 3 - Database of ions and charged molecules. ;;;;; ;;;;; File updated on 2021-03-29 ;;;;; ;;;;; Version: 3.0.0_v1 ;;;;; ;;;;; This collection contains the models included as part of the Martini 3 publication: ;;;;; PCT Souza, et al., Nat. Methods, 2021. DOI: 10.1038/s41592-021-01098-3 ;;;;;;;;; SIMPLE IONS (1 bead) ;;;;;; Sodium ion [moleculetype] ; molname nrexcl NA 1 [atoms] ;id type resnr residu atom cgnr charge 1 TQ5 1 ION NA 1 1.0 ;;;;;; Chloride ion [moleculetype] ; molname nrexcl CL 1 [atoms] ;id type resnr residu atom cgnr charge 1 TQ5 1 ION CL 1 -1.0 35.453 ;;;;;; Bromide ion [moleculetype] ; molname nrexcl BR 1 [atoms] ;id type resnr residu atom cgnr charge mass 1 SQ4 1 ION BR 1 -1.0 79.90 ;;;;;; Iodine ion [moleculetype] ; molname nrexcl IOD 1 [atoms] ;id type resnr residu atom cgnr charge mass 1 SQ2 1 ION ID 1 -1.0 79.90 ;;;;;; Tetramethyl amonium ion [moleculetype] ; molname nrexcl TMA 1 [atoms] ;id type resnr residu atom cgnr charge 1 Q2 1 ION TMA 1 1.0 74.14 ;;;;;; Acetate ion [moleculetype] ; molname nrexcl ACE 1 [atoms] ;id type resnr residu atom cgnr charge 1 SQ5n 1 ION CL 1 -1.0 59.044 ;;;;;; Calcium ion [moleculetype] ; molname nrexcl CA 1 [atoms] ;id type resnr residu atom cgnr charge 1 SD 1 ION CA 1 2.0 40.078 ; TD may be a good option as well. ;;;;;; Tetrafluoroborate ion [moleculetype] ; molname nrexcl BF4 1 [atoms] ;id type resnr residu atom cgnr charge mass 1 Q2 1 ION BF4 1 -1.0 86.80 ;;;;;; Hexafluorophosphate ion [moleculetype] ; molname nrexcl PF6 1 [atoms] ;id type resnr residu atom cgnr charge mass 1 Q1 1 ION PF6 1 -1.0 144.96 ;;;;;; Thiocyanate ion [moleculetype] ; molname nrexcl SCN 1 [atoms] ;id type resnr residu atom cgnr charge mass 1 SQ1 1 ION SCN 1 -1.0 58.08 ;;;;;;;; Perchlorate anion [moleculetype] ; molname nrexcl CLO4 1 [atoms] ;id type resnr residu atom cgnr charge mass 1 Q2 1 ION CLO 1 -1.0 99.45 ;;;;;;;; Nitrate anion [moleculetype] ; molname nrexcl NO3 1 [atoms] ;id type resnr residu atom cgnr charge mass 1 SQ3n 1 ION NO3 1 -1.0 62.005 ;;;;;;;;; BIG IONS USED IN IONIC LIQUIDS ;;;;;; 1-Methyl-3-methylimidazolium ion [moleculetype] ; Name nrexcl MIM 1 [ atoms ] ;id type resnr residu atom cgnr charge mass 1 TN2q 1 MIM SI1 1 0.500 32.38 2 TN2q 1 MIM SI2 2 0.500 32.38 3 TC6 1 MIM SI3 3 0.000 32.38 [constraints] ; i j funct length 2 3 1 0.318 2 1 1 0.318 3 1 1 0.318 ;;;;;; 1-Ethyl-3-methylimidazolium ion [moleculetype] ; Name nrexcl EIM 1 [ atoms ] ;id type resnr residu atom cgnr charge 1 SN2q 1 EIM SI1 1 0.500 46.40 2 TN2q 1 EIM SI2 2 0.500 32.38 3 TC6 1 EIM SI3 3 0.000 32.38 [constraints] ; i j funct length 2 3 1 0.355 2 1 1 0.318 3 1 1 0.318 ;;;;;; 1-Butyl-3-methylimidazolium ion [moleculetype ] ; Name nrexcl BIM 1 [ atoms ] ;id type resnr residu atom cgnr charge mass 1 TN2q 1 BIM SI1 1 0.500 31.37 2 TN2q 1 BIM SI2 2 0.500 32.38 3 TC6 1 BIM SI3 3 0.000 32.38 4 SC3 1 BIM SI4 4 0.000 43.09 [bonds] ; i j funct length force.c. 1 4 1 0.340 7500 [constraints] ; i j funct length 2 3 1 0.318 2 1 1 0.318 3 1 1 0.318 [angles] ; i j k funct angle force.c. 3 1 4 2 120.000 50.0 2 1 4 2 120.000 50.0 [dihedrals] ; i j k l funct angle force.c. 4 2 3 1 2 0.0 200.0 ; ;;;;;; 1-Octyl-3-methylimidazolium ion [moleculetype ] ; Name nrexcl OIM 1 [ atoms ] ;id type resnr residu atom cgnr charge mass 1 TN2q 1 OIM SI1 1 0.500 31.37 2 TN2q 1 OIM SI2 2 0.500 32.38 3 TC6 1 OIM SI3 3 0.000 32.38 4 SC3 1 OIM SI4 4 0.000 43.09 5 C1 1 OIM SI5 4 0.000 57.11 [bonds] ; i j funct length force.c. 1 4 1 0.335 7500 4 5 1 0.410 2500 [constraints] ; i j funct length 2 3 1 0.318 2 1 1 0.318 3 1 1 0.318 [angles] ; i j k funct angle force.c. 3 1 4 2 120.000 50.0 2 1 4 2 120.000 50.0 1 4 5 2 180.000 25.0 [dihedrals] ; i j k l funct angle force.c. 4 2 3 1 2 0.0 200.0 ; ;;;;;; 1-Dodecyl -3-methylimidazolium ion [moleculetype ] ; Name nrexcl DIM 1 [ atoms ] ;id type resnr residu atom cgnr charge mass 1 TN2q 1 DIM SI1 1 0.500 31.37 2 TN2q 1 DIM SI2 2 0.500 32.38 3 TC6 1 DIM SI3 3 0.000 32.38 4 SC3 1 DIM SI4 4 0.000 43.09 5 C1 1 DIM SI5 5 0.000 56.11 6 C1 1 DIM SI6 6 0.000 57.11 [bonds] ; i j funct length force.c. 1 4 1 0.335 7500 4 5 1 0.405 4000 5 6 1 0.475 3800 [constraints] ; i j funct length 2 3 1 0.318 2 1 1 0.318 3 1 1 0.318 [angles] ; i j k funct angle force.c. 3 1 4 2 120.000 50.0 2 1 4 2 120.000 50.0 4 5 6 2 180.000 25.0 [dihedrals] ; i j k l funct angle force.c. 4 2 3 1 2 0.0 200.0 ; ;;;;;; trihexyl(tetradecyl)phoshonium [ moleculetype ] ; Name nrexcl PHO 1 ; 764.002 [ atoms ] ;id type resnr residu atom cgnr charge mass 1 Q1 1 PHO P1 1 1.000 87.08 2 TC3 1 PHO C2 2 0.000 28.05 3 SC2 1 PHO C3 3 0.000 43.09 4 TC3 1 PHO C4 4 0.000 28.05 5 SC2 1 PHO C5 5 0.000 43.09 6 TC3 1 PHO C6 6 0.000 28.05 7 SC2 1 PHO C7 7 0.000 43.09 8 TC3 1 PHO C8 8 0.000 28.05 9 SC2 1 PHO C9 9 0.000 42.08 10 C1 1 PHO C10 10 0.000 56.11 11 C1 1 PHO C11 11 0.000 57.11 [bonds] ; i j funct length force.c. 1 2 1 0.360 5000 2 3 1 0.320 5000 1 4 1 0.360 5000 4 5 1 0.320 5000 1 6 1 0.360 5000 6 7 1 0.320 5000 1 8 1 0.360 5000 8 9 1 0.320 5000 9 10 1 0.440 3800 10 11 1 0.470 3800 [angles] ; i j k funct angle force.c. 2 1 4 2 109.500 200.0 2 1 6 2 109.500 200.0 2 1 8 2 109.500 200.0 4 1 6 2 109.500 200.0 4 1 8 2 109.500 200.0 6 1 8 2 109.500 50.0 1 2 3 2 180.000 25.0 1 4 5 2 180.000 25.0 1 6 7 2 180.000 25.0 1 8 9 2 180.000 25.0 8 9 10 2 180.000 25.0 9 10 11 2 180.000 25.0