Can anyone help me parametrize Si atoms in gromacs forcefields. how can i include parameters in ffnonbonded and bonded and atomtype files of gromacs forcefield for example oplsaa or charmm? (I want to perform md simulation of silica nanoparticles with gromacs and i dont know how)
You can ask the corresponding author of the following paper to share the force field parameters for Si:
The influence of silica nanoparticle geometry on the interfacial interactions of organic molecules: a molecular dynamics study - Physical Chemistry Chemical Physics (RSC Publishing) DOI:10.1039/D1CP04315C
It is a lot easier (with minimum risk) to work with already created one, rather than creating your own.
Ayaz Anwar thanks for your help,after reading the article im trying to install STaGE topology builder which was mentioned in the article, and then use it . i would greatly appreciate to share your experience if you have had a similar one
Sorry, I do not have any experience with STaGE or even Si simulation. I already wrote that it is a lot easier to work with already created/tested topology rather than creating your own. If you want to learn then you need to follow the manual of this software, that will be the place to start.
Plus, again, you can create your own topology and match it against the topology files from that paper. It will give you confidence that the procedure you followed is good.
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