[gmx-users] How to exclude the interactions between molecule A and B in Gromacs?

DeChang Li li.dc06 at gmail.com
Fri Aug 5 05:17:55 CEST 2011

Dear all,

   I want to use Gromacs to run an enhanced sampling molecular dynamics
(ESMD) proposed by Karplus’s group (J. Am. Chem. Soc. (1990) 112, 9161-9175.
& J. Mol. Biol. (1999) 291, 101-115). In the ESMD simulation, we need to
exclude the interactions (especially the Coulomb interactions) between some
small molecules (e.g. ligand A and its replica). How can Gromacs to do this?
Any suggestion will be very appreciated.

Best regards,

Dechang Li, Ph.D
Biomechanics and Biomaterials Laboratory
Department of Applied Mechanics
School of Aerospace Engineering
Beijing Institute of Technology
Beijing 100081, P. R. China
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