[gmx-users] Force field selection for free Bicarbonate molecules in solution

Faulkner, Matthew M.Faulkner at liverpool.ac.uk
Fri Sep 4 13:42:56 CEST 2015

I am trying to find a suitable force field for using Bicarbonate in an aqueous environment in my MDS. I can't find anything where Bicarbonate has been used this way in gromacs in the literature, does anybody know of a reference for me or have advice on which force filed would be best?

I have run several MDS in the OPLS-AA force field for my protein of interest in solution with water and various ions and they work very well,but I would like to add 150 mM HCO3- into my environment. I have a PDB and TOP file prepared using PRODRG for the HCO3- but I'm not sure if the OPLS-AA force field is suitable for this molecule.


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