Dear GROMACS users,
I try to compute energies of a small peptide-domain complex and of its constituents using implicit solvent, so that I can get the binding Delta E. I need the accuracy to be high enough so that I can reliably measure the Delta Delta E between the wildtype peptide and a mutation of it. I would like to get advice as to the best setting and parameters to use; are the ones given below the correct and best ones (most in an mdp file, some run control parameters of GROMACS commands)? Are other defaults in need to be changed? As the GBSA method necessitates using the inexact cut-off interactions, and my system is rather small, I consider using no cut-off at all, i.e. an all-vs.-all approach. For that I understand the parameters should be nstlist=0 ns_type=simple -pd ; in mdrun coulombtype=cut-off rcoulomb=0 vdwtype=cut-off rvdw=0 rlist=0 Then, there are the implicit solvent parameters themselves: implicit_solvent=GBSA gb_algorithm= Still sa_algorithm=Ace-approximation rgbradii=0 Finally, regarding the simulation box, I see no need for periodic boundary conditions, and I pick some big margin around the system (as there are no water molecules, no need to spare): pbc=no -d 5.0 ; in editconf What do you say? Thanks, Ehud.
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