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

[DeChang Li]

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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