In these few days I've done progress on the subject. I employed MKTOP with good results and I minimize the system of 6 molecule of Hexabenzocoronene in a box, creating the topology and running grompp and mdrun with $.mdp.

Now I want to face the problem of solvation (as usual suggestions are welcome) but using as solvent air: Oxygen, Nitrogen and CO2 to start.

On the other hand could be even interesting evaluating the behavior in the traditional solvent, water, adding a level of complexity after to have defined correctly the system.

I did't say nothing about my final goal: simulate the interaction between Spider Proteins of viruses (e.g. SARS-Cov-2) and nanoparticles in the air due to pollution.

Molecular Simulation Methods with Gromacs

www.gromacs.org › deki › files

PDF(although large by simulation standards :-) with 164 residues and a molecular weight of ... This mdp file uses the new interaction cut-off treatment introduced with ... or cheat and open the file rmsf.pdf), which lends further credibility to the ...

Reference Manual - GROMACS documentation

manual.gromacs.org › documentation › manual-2019PDFDec 31, 2018 - Parameterization of novel molecules . ... on algorithms and implementations, see the reference manual part (page 292) of the documentation.

GROMACS Tutorial

www.gromacs.org › deki › files

PDFby JA Lemkul - ‎Cited by 6 - ‎Related articlesparameters for this molecule, and how do we apply them to our system?

Dear Dr. Mitra,

I'm not sure to have understood correctly the first and thirty suggestions. PDF by JA Lemkul is cited into the tutorial?