How to include a itp file to gromacs forcefiled

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Hello
I Have generated silica nanoparticles with charmm-gui and within the zip file there are some .itp file containing information of silica nanoparticles and with pdb file and packmol i generated the my initial structure which i want to perfome md run on it , can anyone help how can i integrate these itp files with charmm forcefield and perform mdrun?

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Hi, you can always include external files with the preprocessor command #include "dir/file.itp". These files can have their own include commands, as often happens with forcefield.itp in standard FF directories.

A few notes - the [ defaults ] section has to come on top; [ atomtypes ] and some other parameters should not be repeated; then usually come [ moleculetype ] definitions; and at the end, you should have [ system ] name and a list of [ molecules ] that corresponds to the quantity and order of molecules in your pdb file.

Gromologist might help you put these things together, as well as produce a self-contained final topology file, but you can also set it all up yourself with a bit of work if you understand the fundamentals.

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@milosz.wieczor thanks for your help
so i should write a topol.top file manually and then include parameters into it or by help of gromologist? considering the fact that my initial structure contains a lot of water and SiO2 molecules writing it manually might take a long time

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@milosz.wieczor and can you help me with gromologist if I want to implement gromologist?

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Yes, you can take an existing .top file and choose whether you want to include the .itps manually or with gromologist. It will depend on, for example, whether you need to merge several parameter files with existing FFs (easier with gromologist) or just put things together (easily done manually).

“A lot of water” is not a problem, if you have 10000 water molecules called SOL, you can simply have

[ molecules ]
SOL 10000

for SiO2, it depends on the connectivity (one big molecule or many small ones?), but you already have an .itp file so your choice will follow from that.

If you describe what your missing parts are, I can guide you in more specific ways.

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thanks a lot for your helps
I have managed to solve this problem with your instructions
thanks a lot