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

Smith, Micholas D. smithmd at ornl.gov
Fri Sep 4 14:27:25 CEST 2015


Quick question, what are you trying to examine with the addition of bicarbonate?


Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Faulkner, Matthew <M.Faulkner at liverpool.ac.uk>
Sent: Friday, September 04, 2015 7:42 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Force field selection for free Bicarbonate molecules in    solution

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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