Dear all,
I need to simulate a salt diluted in a liquid electrolyte.
My experience is with LAMMPS, but so far I only had coarse grained toy models, and setting up the force field was straightforward.
Now I have a real molecule (>20 atoms), which I optimized quantum mechanically with MP2 and I have tried to run various tools to automatically get the parameters: VMD/topotool, ATB+moltemplate. Nothing really works and I need to tweak too many parameters by hand.
So I am wondering whether or not to use an all-atoms design MD software such as Amber or Gromacs. Which one would be the best candidate for my study case considering the physical system? which one is more easy to use when it comes to infer the force field from QM results?
Thank you
Marco
A good staring point is a literature search on similar molecules, and whether there's a mature force field for your kind of molecule. If yes, follow how that force field is *supposed* to be used. If not, some parameterization work is required. I'd guess some general purpose force field is the way to go, such as GAFF, CGenFF. There're plenty tutorials on how to get paramters in the framework of, for example GAFF.
http://ambermd.org/antechamber/gaff.html
Article CHARMM General Force Field: A force field for drug-like mole...
And lastly, good luck.
Marco Di Gennaro
You can start your calculations with GAFF. Just check whether concrete force-fields are available similar to system. If some parameters are missing, you can use Swiss param to generate.
Hi,
you also have LigParGen (http://zarbi.chem.yale.edu/ligpargen/) for the OPLS-AA forcefield.
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