Dear Gromacs users I want to calculate the PMF of tocopherol in DMPC bilayer system. For this means, I used Constraint method. the pull code in my .mdp file is :
pull = constraint pull-geometry = distance ;distance, direction, or cylinder pull-dim = N N Y pull-constr-tol = 1e-6 pull-start = yes ;add current COM distance to pull_init? pull-print-reference = no pull-nstxout = 10000 pull-nstfout = 5 pull-ngroups = 2 pull-ncoords = 1 pull-group1-name = DMPC pull-group2-name = VIT pull-coord1-groups = 1 2 pull-coord1-init = 0.0 In my output file which shows force over time, we have some sudden diverges of force to a very high number. I realized it is because of the boundary condition, one part of molecule comes out of the box and enters from the other side of the box and it needs a huge force to keep the molecule at the same position. Can you please help me how to solve this problem
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