interatomic potentials:
https://www.ctcms.nist.gov/potentials/
https://zhuanlan.zhihu.com/p/351829537
https://www.ctcms.nist.gov/potentials/system/C-H-O/
https://atb.uq.edu.au/index.py?tab=structure_search
https://github.com/dwsideriusNIST/LAMMPS_Examples
opensmog smog2.provides force field generation tool
run simulation under given temperature, pressure and get density
openmm
generate force field on the fly:
from openff.toolkit.topology import Molecule
molecule = Molecule.from_smiles(‘c1ccccc1’)
pymatgen contains polymer generator to lammps:
pymatgen.io.lammps.utils
simulating reaction in molecular dynamics:
implemented in lammps fix bond/react method
random.randomvoidmail@erine.email (pending approval)
seen polymer names on lammps demo website:
https://lammps.org/pictures.html#reactphoto
https://docs.lammps.org/Intro_features.html
If you are a new computational chemist I would advise you to use ASE, it is not only useful for nanoparticles, I’m using it nearly every day.
patent:
http://chemdataextractor.org/results/26088052-3833-41ea-98f1-0a8a3fb2c341
https://www.zhihu.com/question/50559712
moltemplate, packmol
vmd: lammps data file visualization
build input file for lammps:
get retrosynthesis training data on picture search engines
octa: predict polymer properties
https://octa.jp/references/examples/
Link: [5]http://oexchange.org/spec/0.8/rel/related-target
You can try [33]https://spaya.ai/ it is a retro-synthetic analysis
[37]Http://www.orgsyn.org/
[41]Http://www.orgsyn.org/
[45]Http://www.organic-chemistry.org/
Try this interesting blog: [49]http://totallysynthetic.com/blog/
And also this website: [50]http://chemistrybydesign.oia.arizona.edu/
[54]http://www.chemspider.com/
[58]https://pubchem.ncbi.nlm.nih.gov/search
Organic Syntheses Website: <[62]http://www.orgsyn.org
Organic Chemistry Portal: <[63]http://www.organic-chemistry.org/abstracts
Chemsynthesis: [64]http://www.chemsynthesis.com
ChemExper: [65]https://www.chemexper.com
Pub Chem compound: [67]http://pubchem.ncbi.nlm.nih.gov
E-molecules: [68]http://www.emolecules.com
Chemspider: [69]http://www.chemspider.com
Reaxys: [70]https://www.reaxys.com/
SciFinder: [71]http://www.cas.org,
STN: [72]https://stnweb.cas.org/
[80]https://www.vulcanchem.com/
gromacs: creating polymer structure
http://www.gromacs.org/Documentation_of_outdated_versions/How-tos/Polymers
latest gromacs documentation:
https://manual.gromacs.org/documentation/
online organic chemistry textbook:
https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/intro1.htm
openbabel can only run normally on x86 platforms. so do other cheminfo packages.
sources of organic synthesis
https://www.organic-chemistry.org
What is matsci.org?
matsci.org is a community forum for the discussion of anything materials science, with a focus on computational materials science research. Its members are typically from academic research institutions and universities.
People that currently help run matsci.org include maintainers of the following codes and collaborations:
OVITO
GULP
DL_POLY
OPTIMADE
pyiron
hiphive
ASE
MPDS
iFermi
LAMMPS
MaRDA
exciting
JARVIS
and members of the following research groups:
Hacking Materials Group
Persson Group
Materials Virtual Lab
Materials Intelligence
translate bigsmiles into smiles
polymer database:
PolyInfo and NIST Synthetic Polymer MALDI Recipes database
USPEX
chemdraw chemoffice indraw spaya.ai
reaxys scifinder-n
marvin sketch pka
https://github.com/PKUMDL-AI/AutoSynRoute
polymer simulation:
material studio
amsterdam modeling suite
cp2k orca
https://orcaforum.kofo.mpg.de/app.php/portal
chemistry in stack exchange:
https://chemistry.stackexchange.com/
polymer retrosynthesis using retro*:
seq2seq-retro mlp-retro polyretro-uspto
deepchem, chempy(inorganic)
avogadro: import openbabel files
odachi: decompose target molecular into source molecular, highlight the potential bond
rdkit: python chemistry informatic
polymer informatic
ab initio chemistry:
lammps, quantum espresso, nwchem, gamess, uspex
from https://www.webmol.net:
Gamess, Gaussian, MolPro, Mopac, NWChem, Orca, PQS, PSI, Q-Chem, TeraChem, Tinker, Quantum Expresso, and VASP