Dear Gromacs Users, I am trying to study the free energy of binding in a protein-ligand complex.
I use the following pull input in my mdp file: ; Pull code pull = umbrella pull_geometry = distance pull_dim = N Y N pull_start = yes pull_ngroups = 1 pull_group0 = Protein pull_group1 = GLC pull_rate1 = 0.005 pull_k1 = 1000 if I am pulling in 'Y' direction, is it necessary to make sure that the distance between the COM (of the protein and ligand) = distance between the Y coordinates, i.eY(pro)-Y(lig), ? ---- VMD commands ---- set pro [atomselect top "protein"] set glc [atomselect top "resname GLC"] set A [measure center $pro weight mass] 40.33518600463867 35.01163101196289 38.7291374206543 set B [measure center $glc weight mass] 40.591331481933594 39.440189361572266 38.494876861572266 vecdist $A $B 4.4421411021009884 Y(pro)-Y(lig) = 4.42855835 Best, nahren
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