How to deal with a complex molecule?

Dear All

I’m going to simulate a big hydrocarbon molecule (called asphaltene) in aqueous solution. But, because of having diverse atomic structures, no force-field could exactly match its atoms.

So, what should I do? I don’t know how to specify partial chargee?

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Specifying partial charge in LAMMPS is easy. You can either manually edit the 4th column of the “Atoms” section of your LAMMPS data file (or equivalently, the 4th column of the “Data Atoms” section of your moltemplate .LT file, if you use moltemate), or you can use LAMMPS “set” command to control atom charge.

Calculating the partial charge can be another story.

Some force fields, like the original OPLSAA force field, COMPASS, and PCFF, assign partial charges automatically by atom type. (In that case, you only have to use the “set” command to override the charges on the atoms whose charge is not specifies in the force field. …after yove calculated them.)

I think your first step will be to read the published literature to get a sense of what kind of force fields work best for the kinds of molecules you want to simulate. Then choose the simulation software (eg, LAMMPS, OpenMM, GROMACS, MaterialsStudio, NAMD) which has the most convenient molecule builders which support that force field. Technically, you can do (almost) anything I LAMMPS. (It’s more flexible than most other MD programs.) But it might not be easy to use for your purpose. It’s more of a question of convenience.

You might have to compute the partial charges yourself, but the ATB database might be useful for you. The partial charges for the molecules in this database have already been calculated.

Its based on the GROMOS force field, but it works with both the LAMMPS and GROMACS programs.