I'm using Gromacs 5.0.2 for a MD simulation with polymer in a saline solution, but the parameters for the polymers are not know, so I'm using OPLS, but this create a incompatibility with the other components in the simulation.
This is because OPLS is originally developed for a geometric mixing rule for sigma in the LJ 12-6. And the ions and other elements where create with arithmetic rules for sigma.
So, how to combine or adapt in a MD simulation when you have these situation?
Or if there is a set of parameters for polymers that use an arithmetic mixing rule easy to insert in the Gromacs program?
There are three mixing rules defined for GROMACS. I guess OPLS-AA uses Rule no. 3. (Please check the GROMACS Manual (Section 4.1.1 and 5.3.2) for an idea on the mixing rules and the oplsaa forcefield directory that comes installed when you install GROMACS). The potentials defined for the solution/ions should also be based on the same mixing rules. If not, you'll need to keep searching through the literature to get the right parameters.
Here you need to focus on what parameters are more important, i.e. of the polymer or the solution? Once you decide that, you can fix it and try to find potentials for the other for which the mixing rules are same. A random guess would suggest that polymer should be more important as the potentials can greatly change its physics. However, the same can hold true for a solution.
What is the polymer that you are simulating?
Hi thank for responding, I'm simulating a hydrolyzed polyacrylamide. (some CONH2 groups are replaced with COO-). Yes OPLS use the 3rd mixing rule, that is the geometric rule. The problem is that I haven't found parameters for either all geometric or all arithmetic, I was thinking in explicit put the cross parameters if they are geometric and arithmetic, in Gromacs there is a section call [ nonbond_params ] where I can do that.
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Normally you can't mix combination rules. Depending on what else you have in your system it could be easier either to get OPLS parameters for everything else or to use another ff for your polymer. Since the polymer seems to be very simple just use corresponding AMBER types. You can use acpype to generate a topology for monomer - this is very easy and fast.
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