Hello all,
I am trying to pull a small molecule through an ion channel. I have followed the tutorial and generated configurations for the US simulations. Since the distance between the reaction coordinate cannot be more than half the box size, I have splitted the simulations into two sets. Initially, the molecule was at top (start of channel) 30 angstroms and the dummy atom at (origin). In second set, the molecule was at the origin and the dummy atom at 30 angstroms away from molecule in negative y-direction, so that total distance from start is 60. When I use wham to get the pmf, I get pmf from 0 to 30 only. How to combine these two and get a smooth PMF profile from start to end? I have used the below code for pulling to generate configurations.
; Pull code
pull = yes
pull-coord1-dim = N Y N
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_coord1_groups = 1 2
pull_group1_name = HMP
pull_group2_name = DUM
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = direction ; simple distance increase
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = -0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
pull-coord1-vec = 0 -1 0
pull-nstxout = 50
pull-nstfout = 50
pull-print-ref-value = yes
freezegrps = DUM
freezedim = Y Y Y
GROMACS version:
GROMACS modification: Yes/No
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