This zip archive contains all input files and output configurations use to produce molecular dynamics simulations using GROMACS software. The simulations form the basis of an atomistic modelling study of the formation of bioinspired silica materials. It is organised as one folder for each simulation reported in the corresponding publication. The following is a list of all files contained in the archive. input_BIONINSPIRED/ input_BIONINSPIRED/section3.1/ input_BIONINSPIRED/section3.1/P1-DADDn/ input_BIONINSPIRED/section3.1/P1-DADDn/bola12_newtop.itp input_BIONINSPIRED/section3.1/P1-DADDn/em.mdp input_BIONINSPIRED/section3.1/P1-DADDn/md.mdp input_BIONINSPIRED/section3.1/P1-DADDn/mix.gro input_BIONINSPIRED/section3.1/P1-DADDn/mix.top input_BIONINSPIRED/section3.1/P1-DADDn/mix_em.gro input_BIONINSPIRED/section3.1/P1-DADDn/mix_md.gro input_BIONINSPIRED/section3.1/P1-DADDn/mix_npt1.gro input_BIONINSPIRED/section3.1/P1-DADDn/mix_nvt.gro input_BIONINSPIRED/section3.1/P1-DADDn/npt1.mdp input_BIONINSPIRED/section3.1/P1-DADDn/nvt.mdp input_BIONINSPIRED/section3.1/P1-DADDn/oplsaaff.itp input_BIONINSPIRED/section3.1/P1-DADDn/SPC-E.itp input_BIONINSPIRED/section3.1/P1-DADDn/SPC-Eff.itp input_BIONINSPIRED/section3.1/R1-DADDn/ input_BIONINSPIRED/section3.1/R1-DADDn/bola12_newtop.itp input_BIONINSPIRED/section3.1/R1-DADDn/em.mdp input_BIONINSPIRED/section3.1/R1-DADDn/md.mdp input_BIONINSPIRED/section3.1/R1-DADDn/mix_75.top input_BIONINSPIRED/section3.1/R1-DADDn/mix_75_em.gro input_BIONINSPIRED/section3.1/R1-DADDn/mix_75_ext_md.gro input_BIONINSPIRED/section3.1/R1-DADDn/mix_75_ext_md_processed.gro input_BIONINSPIRED/section3.1/R1-DADDn/mix_75_npt1.gro input_BIONINSPIRED/section3.1/R1-DADDn/mix_75_nvt.gro input_BIONINSPIRED/section3.1/R1-DADDn/npt1.mdp input_BIONINSPIRED/section3.1/R1-DADDn/nvt.mdp input_BIONINSPIRED/section3.1/R1-DADDn/oplsaaff.itp input_BIONINSPIRED/section3.1/R1-DADDn/SPC-E.gro input_BIONINSPIRED/section3.1/R1-DADDn/SPC-E.itp input_BIONINSPIRED/section3.1/R1-DADDn/SPC-Eff.itp input_BIONINSPIRED/section3.1/R2-DADDn/ input_BIONINSPIRED/section3.1/R2-DADDn/bola12_newtop.itp input_BIONINSPIRED/section3.1/R2-DADDn/DA+SOL_140_pbc_box.png input_BIONINSPIRED/section3.1/R2-DADDn/em.mdp input_BIONINSPIRED/section3.1/R2-DADDn/md.mdp input_BIONINSPIRED/section3.1/R2-DADDn/mix_140.gro input_BIONINSPIRED/section3.1/R2-DADDn/mix_140.top input_BIONINSPIRED/section3.1/R2-DADDn/mix_140_em.gro input_BIONINSPIRED/section3.1/R2-DADDn/mix_140_md.gro input_BIONINSPIRED/section3.1/R2-DADDn/mix_140_npt1.gro input_BIONINSPIRED/section3.1/R2-DADDn/mix_140_nvt.gro input_BIONINSPIRED/section3.1/R2-DADDn/npt1.mdp input_BIONINSPIRED/section3.1/R2-DADDn/nvt.mdp input_BIONINSPIRED/section3.1/R2-DADDn/oplsaaff.itp input_BIONINSPIRED/section3.1/R2-DADDn/SPC-E.itp input_BIONINSPIRED/section3.1/R2-DADDn/SPC-Eff.itp input_BIONINSPIRED/section3.1/R3-DADDn/ input_BIONINSPIRED/section3.1/R3-DADDn/bola12_newtop.itp input_BIONINSPIRED/section3.1/R3-DADDn/DA+SOL_pbc_193_box.png input_BIONINSPIRED/section3.1/R3-DADDn/em.mdp input_BIONINSPIRED/section3.1/R3-DADDn/md.mdp input_BIONINSPIRED/section3.1/R3-DADDn/mix_193.gro input_BIONINSPIRED/section3.1/R3-DADDn/mix_193.top input_BIONINSPIRED/section3.1/R3-DADDn/mix_193_em.gro input_BIONINSPIRED/section3.1/R3-DADDn/mix_193_md.gro input_BIONINSPIRED/section3.1/R3-DADDn/mix_193_npt1.gro input_BIONINSPIRED/section3.1/R3-DADDn/mix_193_nvt.gro input_BIONINSPIRED/section3.1/R3-DADDn/npt1.mdp input_BIONINSPIRED/section3.1/R3-DADDn/nvt.mdp input_BIONINSPIRED/section3.1/R3-DADDn/oplsaaff.itp input_BIONINSPIRED/section3.1/R3-DADDn/SPC-E.itp input_BIONINSPIRED/section3.1/R3-DADDn/SPC-Eff.itp input_BIONINSPIRED/section3.1/R4-DADDn/ input_BIONINSPIRED/section3.1/R4-DADDn/bola12_newtop.itp input_BIONINSPIRED/section3.1/R4-DADDn/em.mdp input_BIONINSPIRED/section3.1/R4-DADDn/md.mdp input_BIONINSPIRED/section3.1/R4-DADDn/mix_277.gro input_BIONINSPIRED/section3.1/R4-DADDn/mix_277.top input_BIONINSPIRED/section3.1/R4-DADDn/mix_277_em.gro input_BIONINSPIRED/section3.1/R4-DADDn/mix_277_md_ext2.gro input_BIONINSPIRED/section3.1/R4-DADDn/mix_277_npt3.gro input_BIONINSPIRED/section3.1/R4-DADDn/mix_277_nvt.gro input_BIONINSPIRED/section3.1/R4-DADDn/npt1.mdp input_BIONINSPIRED/section3.1/R4-DADDn/nvt.mdp input_BIONINSPIRED/section3.1/R4-DADDn/oplsaaff.itp input_BIONINSPIRED/section3.1/R4-DADDn/SPC-E.itp input_BIONINSPIRED/section3.1/R4-DADDn/SPC-Eff.itp input_BIONINSPIRED/section3.2/ input_BIONINSPIRED/section3.2/P2-DADDn/ input_BIONINSPIRED/section3.2/P2-DADDn/bola12_newtop.itp input_BIONINSPIRED/section3.2/P2-DADDn/DA_layer.gro input_BIONINSPIRED/section3.2/P2-DADDn/em.mdp input_BIONINSPIRED/section3.2/P2-DADDn/md.mdp input_BIONINSPIRED/section3.2/P2-DADDn/mix_DA.top input_BIONINSPIRED/section3.2/P2-DADDn/mix_DA_em.gro input_BIONINSPIRED/section3.2/P2-DADDn/mix_DA_md.gro input_BIONINSPIRED/section3.2/P2-DADDn/mix_DA_md_processed.gro input_BIONINSPIRED/section3.2/P2-DADDn/mix_DA_npt1.gro input_BIONINSPIRED/section3.2/P2-DADDn/mix_DA_nvt.gro input_BIONINSPIRED/section3.2/P2-DADDn/npt1.mdp input_BIONINSPIRED/section3.2/P2-DADDn/nvt.mdp input_BIONINSPIRED/section3.2/P2-DADDn/oplsaaff.itp input_BIONINSPIRED/section3.2/P2-DADDn/SPC-E.itp input_BIONINSPIRED/section3.2/P2-DADDn/SPC-Eff_in_mix.itp input_BIONINSPIRED/section3.2/P3-DADDs/ input_BIONINSPIRED/section3.2/P3-DADDs/bola12_p1.itp input_BIONINSPIRED/section3.2/P3-DADDs/Br.itp input_BIONINSPIRED/section3.2/P3-DADDs/em.mdp input_BIONINSPIRED/section3.2/P3-DADDs/md.mdp input_BIONINSPIRED/section3.2/P3-DADDs/mix.top input_BIONINSPIRED/section3.2/P3-DADDs/mix_md.gro input_BIONINSPIRED/section3.2/P3-DADDs/mix_md_processed.gro input_BIONINSPIRED/section3.2/P3-DADDs/npt1.mdp input_BIONINSPIRED/section3.2/P3-DADDs/nvt.mdp input_BIONINSPIRED/section3.2/P3-DADDs/oplsaaff.itp input_BIONINSPIRED/section3.2/P3-DADDs/out.gro input_BIONINSPIRED/section3.2/P3-DADDs/out_em.gro input_BIONINSPIRED/section3.2/P3-DADDs/out_npt1.gro input_BIONINSPIRED/section3.2/P3-DADDs/out_nvt.gro input_BIONINSPIRED/section3.2/P3-DADDs/SPC-E.itp input_BIONINSPIRED/section3.2/P3-DADDs/SPC-Eff.itp input_BIONINSPIRED/section3.2/P4-DADDd/ input_BIONINSPIRED/section3.2/P4-DADDd/bola12_p2.itp input_BIONINSPIRED/section3.2/P4-DADDd/Br.itp input_BIONINSPIRED/section3.2/P4-DADDd/em.mdp input_BIONINSPIRED/section3.2/P4-DADDd/md.mdp input_BIONINSPIRED/section3.2/P4-DADDd/mix.gro input_BIONINSPIRED/section3.2/P4-DADDd/mix.top input_BIONINSPIRED/section3.2/P4-DADDd/mix_em.gro input_BIONINSPIRED/section3.2/P4-DADDd/mix_md.gro input_BIONINSPIRED/section3.2/P4-DADDd/mix_md_processed.gro input_BIONINSPIRED/section3.2/P4-DADDd/mix_npt1.gro input_BIONINSPIRED/section3.2/P4-DADDd/mix_nvt.gro input_BIONINSPIRED/section3.2/P4-DADDd/npt1.mdp input_BIONINSPIRED/section3.2/P4-DADDd/nvt.mdp input_BIONINSPIRED/section3.2/P4-DADDd/oplsaaff.itp input_BIONINSPIRED/section3.2/P4-DADDd/SPC-E.itp input_BIONINSPIRED/section3.2/P4-DADDd/SPC-Eff.itp input_BIONINSPIRED/section3.2/P5-DADDd/ input_BIONINSPIRED/section3.2/P5-DADDd/bola12_p2.itp input_BIONINSPIRED/section3.2/P5-DADDd/Br.itp input_BIONINSPIRED/section3.2/P5-DADDd/em.mdp input_BIONINSPIRED/section3.2/P5-DADDd/md.mdp input_BIONINSPIRED/section3.2/P5-DADDd/mix.gro input_BIONINSPIRED/section3.2/P5-DADDd/mix.top input_BIONINSPIRED/section3.2/P5-DADDd/mix_em.gro input_BIONINSPIRED/section3.2/P5-DADDd/mix_md.gro input_BIONINSPIRED/section3.2/P5-DADDd/mix_npt1.gro input_BIONINSPIRED/section3.2/P5-DADDd/mix_nvt.gro input_BIONINSPIRED/section3.2/P5-DADDd/npt1.mdp input_BIONINSPIRED/section3.2/P5-DADDd/nvt.mdp input_BIONINSPIRED/section3.2/P5-DADDd/oplsaaff.itp input_BIONINSPIRED/section3.2/P5-DADDd/SPC-E.itp input_BIONINSPIRED/section3.2/P5-DADDd/SPC-Eff.itp input_BIONINSPIRED/section3.2/P9-EXP-reference/ input_BIONINSPIRED/section3.2/P9-EXP-reference/bola12_newtop.itp input_BIONINSPIRED/section3.2/P9-EXP-reference/bola12_p1.itp input_BIONINSPIRED/section3.2/P9-EXP-reference/bola12_p2.itp input_BIONINSPIRED/section3.2/P9-EXP-reference/Br.itp input_BIONINSPIRED/section3.2/P9-EXP-reference/em.mdp input_BIONINSPIRED/section3.2/P9-EXP-reference/md.mdp input_BIONINSPIRED/section3.2/P9-EXP-reference/mix.gro input_BIONINSPIRED/section3.2/P9-EXP-reference/mix.top input_BIONINSPIRED/section3.2/P9-EXP-reference/mix_em.gro input_BIONINSPIRED/section3.2/P9-EXP-reference/mix_md.gro input_BIONINSPIRED/section3.2/P9-EXP-reference/mix_npt.gro input_BIONINSPIRED/section3.2/P9-EXP-reference/mix_nvt.gro input_BIONINSPIRED/section3.2/P9-EXP-reference/npt1.mdp input_BIONINSPIRED/section3.2/P9-EXP-reference/nvt.mdp input_BIONINSPIRED/section3.2/P9-EXP-reference/oplsaaff.itp input_BIONINSPIRED/section3.2/P9-EXP-reference/SPC-E.itp input_BIONINSPIRED/section3.2/P9-EXP-reference/SPC-Eff.itp input_BIONINSPIRED/section3.2/R5-DADDs/ input_BIONINSPIRED/section3.2/R5-DADDs/bola12_p1.itp input_BIONINSPIRED/section3.2/R5-DADDs/Br.itp input_BIONINSPIRED/section3.2/R5-DADDs/DAs+ION_random_142_pbc_box.png input_BIONINSPIRED/section3.2/R5-DADDs/DAs+ION_random_142_pbc_box.tga input_BIONINSPIRED/section3.2/R5-DADDs/em.mdp input_BIONINSPIRED/section3.2/R5-DADDs/md.mdp input_BIONINSPIRED/section3.2/R5-DADDs/mix1.gro input_BIONINSPIRED/section3.2/R5-DADDs/mix1.top input_BIONINSPIRED/section3.2/R5-DADDs/mix1_em.gro input_BIONINSPIRED/section3.2/R5-DADDs/mix1_md.gro input_BIONINSPIRED/section3.2/R5-DADDs/mix1_md_pbc.gro input_BIONINSPIRED/section3.2/R5-DADDs/mix1_npt.gro input_BIONINSPIRED/section3.2/R5-DADDs/mix1_nvt.gro input_BIONINSPIRED/section3.2/R5-DADDs/npt1.mdp input_BIONINSPIRED/section3.2/R5-DADDs/nvt.mdp input_BIONINSPIRED/section3.2/R5-DADDs/oplsaaff.itp input_BIONINSPIRED/section3.2/R5-DADDs/SPC-E.itp input_BIONINSPIRED/section3.2/R5-DADDs/SPC-Eff.itp input_BIONINSPIRED/section3.2/R6-DADDd/ input_BIONINSPIRED/section3.2/R6-DADDd/bola12_p2.itp input_BIONINSPIRED/section3.2/R6-DADDd/Br.itp input_BIONINSPIRED/section3.2/R6-DADDd/em.mdp input_BIONINSPIRED/section3.2/R6-DADDd/md.mdp input_BIONINSPIRED/section3.2/R6-DADDd/mix.gro input_BIONINSPIRED/section3.2/R6-DADDd/mix.top input_BIONINSPIRED/section3.2/R6-DADDd/mix_em.gro input_BIONINSPIRED/section3.2/R6-DADDd/mix_md.gro input_BIONINSPIRED/section3.2/R6-DADDd/mix_npt1.gro input_BIONINSPIRED/section3.2/R6-DADDd/mix_nvt.gro input_BIONINSPIRED/section3.2/R6-DADDd/npt1.mdp input_BIONINSPIRED/section3.2/R6-DADDd/nvt.mdp input_BIONINSPIRED/section3.2/R6-DADDd/oplsaaff.itp input_BIONINSPIRED/section3.2/R6-DADDd/SPC-E.itp input_BIONINSPIRED/section3.2/R6-DADDd/SPC-Eff.itp input_BIONINSPIRED/section3.2/R7-EXP-reference/ input_BIONINSPIRED/section3.2/R7-EXP-reference/bola12_newtop.itp input_BIONINSPIRED/section3.2/R7-EXP-reference/bola12_p1.itp input_BIONINSPIRED/section3.2/R7-EXP-reference/bola12_p2.itp input_BIONINSPIRED/section3.2/R7-EXP-reference/Br.itp input_BIONINSPIRED/section3.2/R7-EXP-reference/em.mdp input_BIONINSPIRED/section3.2/R7-EXP-reference/md.mdp input_BIONINSPIRED/section3.2/R7-EXP-reference/mix.gro input_BIONINSPIRED/section3.2/R7-EXP-reference/mix.top input_BIONINSPIRED/section3.2/R7-EXP-reference/mix_em.gro input_BIONINSPIRED/section3.2/R7-EXP-reference/mix_md.gro input_BIONINSPIRED/section3.2/R7-EXP-reference/mix_md_pbc.gro input_BIONINSPIRED/section3.2/R7-EXP-reference/mix_npt.gro input_BIONINSPIRED/section3.2/R7-EXP-reference/mix_nvt.gro input_BIONINSPIRED/section3.2/R7-EXP-reference/npt1.mdp input_BIONINSPIRED/section3.2/R7-EXP-reference/nvt.mdp input_BIONINSPIRED/section3.2/R7-EXP-reference/oplsaaff.itp input_BIONINSPIRED/section3.2/R7-EXP-reference/SPC-E.itp input_BIONINSPIRED/section3.2/R7-EXP-reference/SPC-Eff.itp input_BIONINSPIRED/section3.3/ input_BIONINSPIRED/section3.3/P6-DADDn-Si/ input_BIONINSPIRED/section3.3/P6-DADDn-Si/bola12_newtop.itp input_BIONINSPIRED/section3.3/P6-DADDn-Si/em.mdp input_BIONINSPIRED/section3.3/P6-DADDn-Si/md.mdp input_BIONINSPIRED/section3.3/P6-DADDn-Si/mix_TMA.gro input_BIONINSPIRED/section3.3/P6-DADDn-Si/mix_TMA.top input_BIONINSPIRED/section3.3/P6-DADDn-Si/mix_TMA_em.gro input_BIONINSPIRED/section3.3/P6-DADDn-Si/mix_TMA_md.gro input_BIONINSPIRED/section3.3/P6-DADDn-Si/mix_TMA_md_processed.gro input_BIONINSPIRED/section3.3/P6-DADDn-Si/mix_TMA_npt1.gro input_BIONINSPIRED/section3.3/P6-DADDn-Si/mix_TMA_nvt.gro input_BIONINSPIRED/section3.3/P6-DADDn-Si/npt1.mdp input_BIONINSPIRED/section3.3/P6-DADDn-Si/nvt.mdp input_BIONINSPIRED/section3.3/P6-DADDn-Si/oplsaaff.itp input_BIONINSPIRED/section3.3/P6-DADDn-Si/Silicates_c10UA.itp input_BIONINSPIRED/section3.3/P6-DADDn-Si/SiOH3.itp input_BIONINSPIRED/section3.3/P6-DADDn-Si/SPC-E.itp input_BIONINSPIRED/section3.3/P6-DADDn-Si/SPC-Eff.itp input_BIONINSPIRED/section3.3/P6-DADDn-Si/TMA_AA.itp input_BIONINSPIRED/section3.3/P7-DADDn-Si/ input_BIONINSPIRED/section3.3/P7-DADDn-Si/bola12_p1.itp input_BIONINSPIRED/section3.3/P7-DADDn-Si/DAs+SI_layer_trans.gro input_BIONINSPIRED/section3.3/P7-DADDn-Si/em.mdp input_BIONINSPIRED/section3.3/P7-DADDn-Si/md.mdp input_BIONINSPIRED/section3.3/P7-DADDn-Si/mix_SIOH3.gro input_BIONINSPIRED/section3.3/P7-DADDn-Si/mix_SIOH3.top input_BIONINSPIRED/section3.3/P7-DADDn-Si/mix_SIOH3_em.gro input_BIONINSPIRED/section3.3/P7-DADDn-Si/mix_SIOH3_md.gro input_BIONINSPIRED/section3.3/P7-DADDn-Si/mix_SIOH3_md_processed.gro input_BIONINSPIRED/section3.3/P7-DADDn-Si/mix_SIOH3_npt1.gro input_BIONINSPIRED/section3.3/P7-DADDn-Si/mix_SIOH3_nvt.gro input_BIONINSPIRED/section3.3/P7-DADDn-Si/npt1.mdp input_BIONINSPIRED/section3.3/P7-DADDn-Si/nvt.mdp input_BIONINSPIRED/section3.3/P7-DADDn-Si/oplsaaff.itp input_BIONINSPIRED/section3.3/P7-DADDn-Si/Silicates_c10UA.itp input_BIONINSPIRED/section3.3/P7-DADDn-Si/SiOH3_O.itp input_BIONINSPIRED/section3.3/P7-DADDn-Si/SPC-E.itp input_BIONINSPIRED/section3.3/P7-DADDn-Si/SPC-Eff.itp input_BIONINSPIRED/section3.3/P8-DADDn-Si/ input_BIONINSPIRED/section3.3/P8-DADDn-Si/bola12_p2.itp input_BIONINSPIRED/section3.3/P8-DADDn-Si/em.mdp input_BIONINSPIRED/section3.3/P8-DADDn-Si/md.mdp input_BIONINSPIRED/section3.3/P8-DADDn-Si/npt1.mdp input_BIONINSPIRED/section3.3/P8-DADDn-Si/npt2.mdp input_BIONINSPIRED/section3.3/P8-DADDn-Si/nvt.mdp input_BIONINSPIRED/section3.3/P8-DADDn-Si/oplsaaff.itp input_BIONINSPIRED/section3.3/P8-DADDn-Si/out2.gro input_BIONINSPIRED/section3.3/P8-DADDn-Si/out2.top input_BIONINSPIRED/section3.3/P8-DADDn-Si/out2_em.gro input_BIONINSPIRED/section3.3/P8-DADDn-Si/out2_md.gro input_BIONINSPIRED/section3.3/P8-DADDn-Si/out2_md_processed.gro input_BIONINSPIRED/section3.3/P8-DADDn-Si/out2_npt1.gro input_BIONINSPIRED/section3.3/P8-DADDn-Si/out2_npt2.gro input_BIONINSPIRED/section3.3/P8-DADDn-Si/out2_nvt.gro input_BIONINSPIRED/section3.3/P8-DADDn-Si/Silicates_c10UA.itp input_BIONINSPIRED/section3.3/P8-DADDn-Si/SiOH3.itp input_BIONINSPIRED/section3.3/P8-DADDn-Si/SPC-E.itp input_BIONINSPIRED/section3.3/P8-DADDn-Si/SPC-Eff.itp input_BIONINSPIRED/section3.4/ input_BIONINSPIRED/section3.4/P10-EXP-monomeric/ input_BIONINSPIRED/section3.4/P10-EXP-monomeric/bola12_newtop.itp input_BIONINSPIRED/section3.4/P10-EXP-monomeric/bola12_p1.itp input_BIONINSPIRED/section3.4/P10-EXP-monomeric/bola12_p2.itp input_BIONINSPIRED/section3.4/P10-EXP-monomeric/em.mdp input_BIONINSPIRED/section3.4/P10-EXP-monomeric/md.mdp input_BIONINSPIRED/section3.4/P10-EXP-monomeric/mix.gro input_BIONINSPIRED/section3.4/P10-EXP-monomeric/mix.top input_BIONINSPIRED/section3.4/P10-EXP-monomeric/mix_em.gro input_BIONINSPIRED/section3.4/P10-EXP-monomeric/mix_md.gro input_BIONINSPIRED/section3.4/P10-EXP-monomeric/mix_npt.gro input_BIONINSPIRED/section3.4/P10-EXP-monomeric/mix_nvt.gro input_BIONINSPIRED/section3.4/P10-EXP-monomeric/npt1.mdp input_BIONINSPIRED/section3.4/P10-EXP-monomeric/nvt.mdp input_BIONINSPIRED/section3.4/P10-EXP-monomeric/oplsaaff.itp input_BIONINSPIRED/section3.4/P10-EXP-monomeric/Silicates_c10UA.itp input_BIONINSPIRED/section3.4/P10-EXP-monomeric/SiOH3.itp input_BIONINSPIRED/section3.4/P10-EXP-monomeric/SiOH4.itp input_BIONINSPIRED/section3.4/P10-EXP-monomeric/SPC-E.itp input_BIONINSPIRED/section3.4/P10-EXP-monomeric/SPC-Eff.itp input_BIONINSPIRED/section3.4/P10-EXP-monomeric/TMA_AA.itp