I am currently working on inorganic surfaces like silica, calcite etc. I have the values for the parameters, but I don't know how to generate the topology file. As it is a non-standard molecule, I simply cannot use the pdb2gmx command for topology generation.
The information given in the gromacs manual is also quite confusing. It would be helpful if someone could share a tutorial (not silica exactly, but any general purpose tutorial will do).
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