GROMACS version:2022.5
GROMACS modification: Yes/No
I have performed the umbrella sampling simulations by pulling the protein away from the membrane.
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = PROTEIN
pull_group2_name = ECLIP
pull-pbc-ref-prev-step-com = yes
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.005 ; 0.005 nm per ps
pull_coord1_k = 5000 ; kJ mol^-1 nm^-2
I got the PMF, but it did not show the potential well. To get the well, I want to pull it towards the membrane. Initially, my reference point was the protein COM and the membrane upper leaflet headgroup COM. When I pull the protein towards the membrane by setting
pull_coord1_rate = -0.005 ; 0.005 nm per ps
I get the error
Pull reference distance for coordinate 1 (-0.000041) needs to be non-negative
I suppose it’s because the protein is trying to cross the reference and, hence, getting a negative distance. Should I change the reference to the lower leaflet COM and pull it?
Will it cause an error in the WHAM calculation because changing the reference will make the distances inconsistent?