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Allowing automated atom typing for larger system(>=100 molecules) upon providing the exact coeff. for each atom,bond,angle,dihedral,impropers,etc. for it's smaller individual component( 1 molecule) .data file #569

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amannsonii3 opened this issue Jun 20, 2024 · 1 comment

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@amannsonii3
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@amannsonii3 amannsonii3 changed the title Sometimes when foyer troubles with multiple atom-typing (specially for cyclic structures, for linear it works great) Allowing automated atom typing for larger system(100 molecules) upon provide atom-typed coeff.(not the opls value, but the exact coeff. for each atom,bond,angle,dihedral,impropers,etc.) for it's smaller individual component( 1 molecule) Jun 20, 2024
@amannsonii3
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I find foyer struggles with cyclic structures(I tried Ethylene Carbonate(EC) and Propylene Carbonate(PC)) more, than linear structures(dimethyl Carbonate(DMC) or ethyl methyl carbonate(EMC)) for atom typing.
It finds multiple atom types for EC and PC, even though the exact parameters {Lucienne's param.} exist for PC specifically.

When I tried commenting on the confused atom types from the. XML forcefield file generates errors like the expected 17 bond angle parameters, but only 16 are found.

Since mBuild can easily build a box with the required molecules, I request a way to iterate over the molecules and assign them the parameter from what I supply for 1 such molecule. And expanding this to a system constituting different molecules. If one wants to use their own parameters, they can do so only after the foyer builds that file right and changes the .data file

But what if the foyer fails to build the .data file to begin with?

Pardon me if such a feature already exists, I just started out with research in MD(still an undergrad)

@amannsonii3 amannsonii3 changed the title Allowing automated atom typing for larger system(100 molecules) upon provide atom-typed coeff.(not the opls value, but the exact coeff. for each atom,bond,angle,dihedral,impropers,etc.) for it's smaller individual component( 1 molecule) Allowing automated atom typing for larger system(>=100 molecules) upon providing the exact coeff. for each atom,bond,angle,dihedral,impropers,etc. for it's smaller individual component( 1 molecule) .data file Jun 27, 2024
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