[gmx-users] PMF calculation_ Constraint

Sepideh Kavousi skavou1 at tigers.lsu.edu
Tue Sep 22 21:46:19 CEST 2015

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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