My group works with the bicarbonate and similar anions in the context of CO2 chemisorption.
You must exercise serious caution to assign correct electrostatic potential at the surface of the anion and account for hydration/solvation effects within the force field derivation procedure. On Fri, Sep 4, 2015 at 8:42 AM, Faulkner, Matthew <[email protected]> wrote: > 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. > > Regards, > Matthew. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
