Grain boundary:
http://aimsgb.org (https://github.com/ksyang2013/aimsgb)
https://stabix.readthedocs.io/en/latest/
FEM + MD:
Interactive MD:
https://physics.weber.edu/schroeder/md/
Lectures:
http://people.virginia.edu/~lz2n/mse627/
http://www.fisica.uniud.it/~ercolessi/md/md/md.html
http://www.ch.embnet.org/MD_tutorial/
http://www.physics.udel.edu/~bnikolic/teaching/phys660/lectures.html
http://www.eng.buffalo.edu/~kofke/ce530/index.html
https://www.rocq.inria.fr/matherials/spip.php?rubrique114
http://lammps.sandia.gov/tutorials.html
http://web.mit.edu/mbuehler/www/Teaching/overview.htm
http://people.virginia.edu/~lz2n/mse627/
https://events.prace-ri.eu/event/391/
http://www.archer.ac.uk/training/course-material/2015/06/MolDy_Strath/
http://research.chem.psu.edu/shsgroup/chem647/newNotes/node1.html
http://www.acclab.helsinki.fi/~knordlun/
Potentials:
http://www.ctcms.nist.gov/potentials/
https://sites.google.com/site/akohlmey/
https://openkim.org/
https://openkim.org/kim-items/models/by-species#Fe
Downloads:
http://www.ks.uiuc.edu/Research/vmd/imd/
http://www.diffpy.org/
http://www.ctcms.nist.gov/potentials/Download/
http://lammps.sandia.gov/movies.html
https://icme.hpc.msstate.edu/mediawiki/index.php/Category:LAMMPS
http://www.numericalsolutions.org/software.html
http://mdlab.sourceforge.net/
http://lcls.crc.nd.edu/joomla/index.php/software
http://www.szfki.hu/~nphys/rmcsans++/AtomEye.html
http://li.mit.edu/Archive/Graphics/A/
http://imagej.nih.gov/ij/
https://www.scientificlinux.org/
http://www.ddcode.com/free-download-physics-live-cd/3-227249.html
http://www.z-cam.es/software.php
https://sites.google.com/site/zrftum/home/links
http://www.jwave.vt.edu/crcd/archives/
http://www-stone.ch.cam.ac.uk/
Long time MD:
http://theory.cm.utexas.edu/eon/index.html
http://cdp.ornl.gov/EFRCschool/pdf/talks/Perez_tutorial.pdf
http://www.mpipks-dresden.mpg.de/~bemod12/Slides/
Video:
http://helper.ipam.ucla.edu/videos.aspx
MD using Matlab:
http://www.cchem.berkeley.edu/chem195/index.html
http://people.sc.fsu.edu/~jburkardt/m_src/md/md.html
http://people.sc.fsu.edu/~jburkardt/
http://karin.fq.uh.cu/qct/
http://karin.fq.uh.cu/qct/Tema_03/03.01.Din%E1mica%20molecular%20con%20potenciales%20cl%E1sicos/MD-working_material.pdf
Understanding LAMMPS:
http://phelafel.technion.ac.il/~bbliron/manual.html
https://wiki.fysik.dtu.dk/ase/ase/calculators/lammps.html#module-ase.calculators.lammps
Molecular dynamics blog:
http://moleculardynamicsstudio.blogspot.in/
http://www.modelingmaterials.org/
Others:
http://stabix.readthedocs.org/en/latest/
http://www.softsimu.net/downloads.shtml
https://simtk.org/home/openmm
https://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling
Visualisation:
http://dxa.ovito.org/download.html
http://dxa.ovito.org/tutorial_lammps/index.html
Examples:
http://www.jwave.vt.edu/crcd/archives/StProjs98/
http://www.jwave.vt.edu/crcd/
https://courses.physics.illinois.edu/phys466/sp2013/projects/
Python:
http://materialsinnovation.github.io/pymks/
https://wiki.fysik.dtu.dk/ase/tutorials/tutorials.html
Tools:
https://debyer.readthedocs.org/en/latest/ (XRD)
http://atomsk.univ-lille1.fr/ (atomistic transformations)
DFT/Ab Initio MD:
http://www.quantum-espresso.org/
http://www.abinit.org/
http://cpmd.org/
http://www.msg.chem.iastate.edu/gamess/
https://www.vasp.at/
Radiation Softwares:
http://www.srim.org/
http://www.fluka.org/fluka.php
https://laws.lanl.gov/vhosts/mcnp.lanl.gov/references.shtml#mcnp6_refs
https://asc.llnl.gov/computing_resources/purple/archive/benchmarks/mdcask/
Tutorial:
http://www.helsinki.fi/~koehenri/work/www_gradu/gradu_html/node1.html
Kedharnath's Site 