I generally work on fluid flow, so some basic concepts in chemistry are new to me. Work I'm doing requires use of molecular dynamics (MD) to do classical potential simulations of water–NaCl systems but this question is about water models more than simulation and software details.
The simulations require definition of a "water model." There's apparently one already implemented in an example/tutorial I'm using (below). I want to compare the results of simulations based on different water models. My problem is that I'm having a lot of trouble understanding how to change my water model (which I think is SPC/E) because I don't really understand what it is.
I have found tables that provide parameters for different water models, like this table at Wikipedia: https://en.wikipedia.org/wiki/Water_model
However, when I look at my software, I can't relate what I'm seeing to the table. I can't find an example of where someone has taken information from this sort of table and explained how to implement it in a simulation. So my first request is, please point me to anything out there! Here's the part of my software that I think defines my water model:
&FORCEFIELD &BEND ATOMS H O H K 0. THETA0 1.8 &END BEND &BEND ATOMS O H H K 0. THETA0 1.8 &END BEND &BOND ATOMS O H K 0. R0 1.8 &END BOND &BOND ATOMS H H K 0. R0 1.8 &END BOND &CHARGE ATOM O CHARGE -0.8476 &END CHARGE &CHARGE ATOM H CHARGE 0.4238 &END CHARGE &NONBONDED &LENNARD-JONES ATOMS O O EPSILON 78.198 ! this is K, = 0.155 kcal/mol = 0.650 kJ/mol SIGMA 3.166 RCUT 11.4 &END LENNARD-JONES &LENNARD-JONES ATOMS O H EPSILON 0.0 SIGMA 3.6705 RCUT 11.4 &END LENNARD-JONES &LENNARD-JONES ATOMS H H EPSILON 0.0 SIGMA 3.30523 RCUT 11.4 &END LENNARD-JONES &END NONBONDED &END FORCEFIELD
I can generally see that everything up to &NONBONDED relates to water somehow because it's about charge, H, and O (I have no idea what "K" is). But what about the "LENNARD-JONES" stuff? I know in general what a Lennard Jones model is, but cannot see how that would be related to water models. If it is, how? Thank you for any advice on how to understand this.