Dear Lammps users,
Hope you all are well.
I need to use implicit solvent (water) in my simulation, but I couldn’t find out how it works. As I know there is no water molecule in the simulation box when we want to consider the solvent as an implicit form. However, I don’t know how to define the solvent in such a model.
As I went through the internet and Lammps manual, I found “pair_style coul/diel cutoff” and "pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
" as examples.
Is it enough to just define the pair coeff in one of these ways?
Do I have to do more things?
First you have to look up and figure out which implicit solvent model you want to implement. There are quite a few.
What LAMMPS has is very minimal and not likely to work well for implicit water.
Chances are, that you will be better off with an MD code that has a better implicit water model built in like NAMD or Amber.
The type of model is not important in this step for me. I just want to know how to implement it on Lammps.
Please let me know an overview of using implicit solvent with Lammps because I couldn’t find a concrete information on documents and websites.
sorry, but you cannot “implement it” when you don’t know what it is.
if you don’t care what the result is, you don’t need to do a simulation.
the usual way to set up a LAMMPS simulation is:
- decide on the model
- figure out what functional forms, i.e. potential functions, are required by that model
- look up which of the potentials in LAMMPS can implement those, if any
- look up the parameters you need to set for the material you want to model from a publication that describes such a model (or learn how to derive such parameters).
whether this is with an implicit solvent or something else doesn’t matter.