Two tools to generate the input files for LAMMPS, DL_POLY or GROMACS to produce the initial structure

https://github.com/agiliopadua/fftool
http://m3g.iqm.unicamp.br/packmol/home.shtml

Open Babel

https://open-babel.readthedocs.io/en/latest/Installation/install.html#install-binaries

Basic Geometry Optimization and Packmol Packaging Tutorial

https://www.youtube.com/watch?v=Bk96DOEhECw&feature=youtu.be&fbclid=IwAR1PNoK6cZ7ytL31_kNdcxeqfJonIUjkzg54fO42173iAwANF3l9_NBbXoU

MDAnalysis

https://www.mdanalysis.org/UserGuide/index.html

Amber force field單位轉換到Gromacs

For non-bonded:

• εgro=εGAFF·4.184
• σgro=RGAFF·25/6  * 1/10 = 0.17818·RGAFF

For bonded:

• Bonds: b0gro = b0GAFF / 10   ;    kb,gro = kb,GAFF /10 *2 *4.184
• Angles: Egro = Emin/2 cth = EGAFF *2 * 4.184
• Dihedrals: kdgro = PKGAFF * 4.184 / IDIVFGAFF

參考

https://gcm.upc.edu/en/members/luis-carlos/molecular-dynamics
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-September/101115.html
https://github.com/lanl/gromacs-kokkos/blob/master/src/gromacs/math/units.h

Gromacs

download
http://manual.gromacs.org/documentation/current/download.html

install
https://scc.ustc.edu.cn/xwgg/201810/W020181022366453106481.pdf

force field
https://github.com/gromacs/gromacs/tree/master/share/template