forcefield_for_conjugated_polymers
Forcefield files for modelling conjugated polymers using Molecular Dynamics
https://github.com/nicholas9182/forcefield_for_conjugated_polymers
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
○Academic publication links
-
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (2.1%) to scientific vocabulary
Repository
Forcefield files for modelling conjugated polymers using Molecular Dynamics
Basic Info
- Host: GitHub
- Owner: nicholas9182
- Language: Shell
- Default Branch: main
- Size: 16.1 MB
Statistics
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 1
- Releases: 2
Metadata Files
README.md
Folders containing relevant files for FF development for OBT
Residue names
MONOMERS AND SMALL MOLECULES
HG = hydrogen-terminated monomer with glycol side chains \ HA = hydrogen-terminated monomer with alkyl side chains \ GS = tin-terminated monomer (Sn Me3 terminated) with glycol sidechains \ GB = Bromine terminated monomer with glycol sidechains \ AS = tin-terminated monomer (Sn Me3 terminated) with alkylated sidechains \ AB = Bromine terminated monomer with alkylated sidechains \ CT = Crown ether monomer with Br terminals and tri-ethelyn glycol side chains \ CQ = Crown ether monomer with Br terminals and quad-ethelyn glycol side chains \ TF = Tetrahydrofuran \ TB = Tetraphenylborate \ PC = Perchlorate \ AN = Acetonitrile \ CF = Chloroform \ PF = Hexa fluoro phosphate \ TA = TBA \ GT = Triethylene oxybithiophene unit capped with thiophenes each end \ GG = Four thiophenes with two triethylene glycol side chains on the same unit
OXYBITHIOPHENE UNITS ##
GI = glycolated sidechains, first unit \ GM = glycolated sidechains, middle unit \ GE = glycolated sidechains, end unit \ AI = alkylated sidechains, first unit \ AM = alkylated sidechains, middle unit \ AE = alkylated sidechains, end unit \ MI = Glycolated with methyl spacer, first unit \ MM = Glycolated with methyl spacer, middle unit \ ME = Glycolated with methyl spacer, end unit \ EI = Glycolated with ethyl spacer, first unit \ EM = Glycolated with ethyl spacer, middle unit \ EE = Glycolated with ethyl spacer, end unit \ PI = Glycolated with propyl spacer, first unit \ PM = Glycolated with propyl spacer, first unit \ PE = Glycolated with propyl spacer, first unit \ BI = Glycolated with butyl spacer, first unit \ BM = Glycolated with butyl spacer, middle unit \ BE = Glycolated with butyl spacer, end unit \ NI = Glycolated with pentyl spacer, first unit \ NM = Glycolated with pentyl spacer, middle unit \ NE = Glycolated with pentyl spacer, end unit \ HI = Glycolated with hexyl spacer, first unit \ HM = Glycolated with hexyl spacer, middle unit \ HE = Glycolated with hexyl spacer, end unit
MIXED SIDECHAIN LENGTH MONOMERS ##
A0 = Glycolated with sidechain length 0, start unit \ B0 = Glycolated with sidechain length 0, middle unit \ C0 = Glycolated with sidechain length 0, last unit \ B6 = Glycolated with sidechain length 6, last unit \ A1 = Glycolated with sidechain length 1, start unit \ B1 = Glycolated with sidechain length 1, middle unit \ C1 = Glycolated with sidechain length 1, last unit \ A2 = Glycolated with sidechain length 2, start unit \ B2 = Glycolated with sidechain length 2, middle unit \ C2 = Glycolated with sidechain length 2, last unit \ A4 = Glycolated with sidechain length 4, start unit \ B4 = Glycolated with sidechain length 4, middle unit \ C4 = Glycolated with sidechain length 4, last unit \ A5 = Glycolated with sidechain length 5, start unit \ B5 = Glycolated with sidechain length 5, middle unit \ C5 = Glycolated with sidechain length 5, last unit \ A6 = Glycolated with sidechain length 6, start unit \ B6 = Glycolated with sidechain length 6, middle unit \ C6 = Glycolated with sidechain length 6, last unit
OXYBITHIOPHENES WITH BACKBONE AND SIDECHAIN SPACERS ##
OI = glycolated sidechains with thiophene backbone spacer, first unit \ OM = glycolated sidechains with thiophene backbone spacer, middle unit \ II = glycolated sidechains with thienothiophene backbone spacer, first unit \ IM = glycolated sidechains with thienothiophene backbone spacer, middle unit \ SI = glycolated sidechains with thiophene backbone spacer and methyl sc spacer, first unit \ SM = glycolated sidechains with thiophene backbone spacer and methyl sc spacer, middle unit \ TI = glycolated sidechains with thienothiophene backbone spacer and methyl sc spacer, first unit \ TM = glycolated sidechains with thienothiophene backbone spacer and methyl sc spacer, middle unit \ UI = glycolated sidechains with thiophene backbone spacer and ethyl sc spacer, first unit \ UM = glycolated sidechains with thiophene backbone spacer and ethyl sc spacer, middle unit \ VI = glycolated sidechains with thienothiophene backbone spacer and ethyl sc spacer, first unit \ VM = glycolated sidechains with thienothiophene backbone spacer and ethyl sc spacer, middle unit \ WI = glycolated sidechains with thiophene backbone spacer and propyl sc spacer, first unit \ WM = glycolated sidechains with thiophene backbone spacer and propyl sc spacer, middle unit \ XI = glycolated sidechains with thienothiophene backbone spacer and propyl sc spacer, first unit \ XM = glycolated sidechains with thienothiophene backbone spacer and propyl sc spacer, middle unit \ YI = glycolated sidechains with thiophene backbone spacer and butyl sc spacer, first unit \ YM = glycolated sidechains with thiophene backbone spacer and butyl sc spacer, middle unit \ YE = glycolated sidechains with thiophene backbone spacer and butyl sc spacer, end unit \ ZI = glycolated sidechains with thienothiophene backbone spacer and butyl sc spacer, first unit \ ZM = glycolated sidechains with thienothiophene backbone spacer and butyl sc spacer, middle unit \ LI = glycolated sidechains with thiophene backbone spacer and pentyl sc spacer, first unit \ LM = glycolated sidechains with thiophene backbone spacer and pentyl sc spacer, middle unit \ CI = glycolated sidechains with thienothiophene backbone spacer and pentyl sc spacer, first unit \ CM = glycolated sidechains with thienothiophene backbone spacer and pentyl sc spacer, middle unit \ DI = glycolated sidechains with thiophene backbone spacer and hexyl sc spacer, first unit \ DM = glycolated sidechains with thiophene backbone spacer and hexyl sc spacer, middle unit \ FI = glycolated sidechains with thienothiophene backbone spacer and hexyl sc spacer, first unit \ FM = glycolated sidechains with thienothiophene backbone spacer and hexyl sc spacer, middle unit
GLYCOLATED BITHIOPHENES WITH BACKBONE AND SIDECHAIN SPACERS INVERTED ##
M1 = Methyl end, first unit \ M2 = Methyl end, middle unit \ M3 = Methyl end, end unit \ E1 = Ethyl end, first unit \ E2 = Ethyl end, middle unit \ E3 = Ethyl end, end unit \ P1 = Propyl end, first unit \ P2 = Propyl end, middle unit \ P3 = Propyl end, end unit \ U1 = Butyl end, first unit \ U2 = Butyl end, middle unit \ U3 = Butyl end, end unit \ N1 = Pentyl end, first unit \ N2 = Pentyl end, middle unit \ N3 = Pentyl end, end unit \ H1 = Hexyl end, first unit \ H2 = Hexyl end, middle unit \ H3 = Hexyl end, end unit \ S1 = Heptyl end, first unit \ S2 = Heptyl end, middle unit \ S3 = Heptyl end, end unit \ SA = Thiophene backbone spacer and methyl end, first unit \ SB = Thiophene backbone spacer and methyl end, middle unit \ NA = Thiophene backbone spacer and ethyl end, first unit \ NB = Thiophene backbone spacer and ethyl end, middle unit \ UA = Thiophene backbone spacer and propyl end, first unit \ UB = Thiophene backbone spacer and propyl end, middle unit \ VA = Thiophene backbone spacer and butyl end, first unit \ VB = Thiophene backbone spacer and butyl end, middle unit \ WA = Thiophene backbone spacer and pentyl end, first unit \ WB = Thiophene backbone spacer and pentyl end, middle unit \ XA = Thiophene backbone spacer and hexyl end, first unit \ XB = Thiophene backbone spacer and hexyl end, middle unit \ YA = Thiophene backbone spacer and heptyl end, first unit \ YB = Thiophene backbone spacer and heptyl end, middle unit \ ZA = Thienophene backbone spacer and methyl end, first unit \ ZB = Thienophene backbone spacer and methyl end, middle unit \ LA = Thienophene backbone spacer and ethyl end, first unit \ LB = Thienophene backbone spacer and ethyl end, middle unit \ CA = Thienophene backbone spacer and propyl end, first unit \ CB = Thienophene backbone spacer and propyl end, middle unit \ D1 = Thienophene backbone spacer and butyl end, first unit \ DB = Thienophene backbone spacer and butyl end, middle unit \ FA = Thienophene backbone spacer and pentyl end, first unit \ FB = Thienophene backbone spacer and pentyl end, middle unit \ OA = Thienophene backbone spacer and hexyl end, first unit \ OB = Thienophene backbone spacer and hexyl end, middle unit \ IA = Thienophene backbone spacer and heptyl end, first unit \ IB = Thienophene backbone spacer and heptyl end, middle unit
NDI POLYMER UNITS ##
I1 = glycolated bithiophene first unit \ I2 = glycolated bithiophene middle unit \ I3 = glycolated bithiophene end unit \ I4 = NDI alkylated unit middle unit \ I5 = NDI glycolated unit middle unit \ I6 = NDI with triethylene glycolated monomer
NDI SINGLE UNITS
I7 = NDI alkylated unit monomer with one side chain ND1 = T-aNDI-T with C12C8 sidechains ND2 = T-aNDI-T with C20 sidechains ND3 = T-gNDI-T with g7 sidechains ND4 = T-gNDI-T with g7 sidechains polaron ND5 = T-gNDI-T with g7 sidechains bipolaron ND6 = T-gNDI-T with C20 sidechains polaron ND7 = T-gNDI-T with C20 sidechains bipolaron ND8 = T-gNDI-T with C12C8 sidechains polaron ND9 = T-gNDI-T with C12C8 sidechains bipolaron NDA = T-gNDI-T with g4g4 sidechains NDB = T-gNDI-T with g3g3 sidechains
DPP AND VINYL POLYMER UNITS ##
D01 = DPP-TTT first unit \ D02 = DPP-TTT middle unit \ D03 = DPP-TTT end unit \ D04 = gDPP-TTT first unit \ D05 = gDPP-TTT middle unit \ D06 = gDPP-TTT end unit \ D07 = DPP-TTVTT first unit \ D08 = DPP-TTVTT middle unit \ D09 = DPP-TTVTT end unit \ D10 = gDPP-TTVTT first unit \ D11 = gDPP-TTVTT middle unit \ D12 = gDPP-TTVTT end unit \ D13 = DPPTF monomer \ D14 = DPPTT monomer \ D15 = DPPTN monomer
MONOMERS WITH NO PARTIAL CHARGES ##
GIn = glycolated sidechains, first unit \ GMn = glycolated sidechains, middle unit \ GEn = glycolated sidechains, end unit \ AIn = alkylated sidechains, first unit \ AMn = alkylated sidechains, middle unit \ AEn = alkylated sidechains, end unit
pBTTT
T1 = pBTTT first unit \ T2 = pBTTT middle unit \ T3 = pbTTT end unit \ T4 = gpBTTT first unit \ T5 = gpBTTT middle unit \ T6 = gpbTTT end unit \ T7 = teg pgT2-TT first unit \ T8 = teg pgT2-TT middle unit \ T9 = teg pgT2-TT end unit \
BBL monomer units
CBM = cis perinone BBL monomer analogue TBM = trans perinone BBL monomer analogue
Owner
- Name: Nicholas Siemons
- Login: nicholas9182
- Kind: user
- Repositories: 2
- Profile: https://github.com/nicholas9182
Citation (CITATION.cff)
cff-version: 1.0.0
message: "If you use this forcefield, please cite it as below."
authors:
- family-names: Siemons
given-names: Nicholas
orcid: https://orcid.org/0000-0002-0755-3981
title: "Forcefield for modelling Mixed Transport Polymers"
version: 1.0.0
doi: 10.5281/zenodo.8011644
date-released: 2023-06-06