[gmx-users] Cylinder option in pull code
D.O-Neill at warwick.ac.uk
Mon Nov 7 11:39:59 CET 2016
I am using the pull code in Gromacs 4.5.4, to constrain the distance (z) between a small molecule and a lipid bilayer. I have included the pull_geometry = cylinder option as I wanted to limit the small molecule's movement in the x and y directions. My understanding was that the radius of the cylinder would provide such a limitation, but after checking the trajectory and plotting the coordinates of the COM over time (using g_traj), it is clear that the molecule is constrained in z but still has complete freedom in x and y.
Is there something wrong in my setup? Or am I misunderstanding how this cylinder option works and what it is designed for?
Pull parameters are listed below.
; Pull code
pull = constraint
pull_geometry = cylinder
pull_dim = N N Y
pull_r1 = 1
pull_r0 = 1.5
pull_start = yes
pull_ngroups = 1
pull_group0 = A
pull_group1 = FRE2
pull_init1 = 0
pull_vec1 = 0 0 1
pull_rate1 = 0
pull_k1 = 1000 ; kJ mol^-1 nm^-2
pull_nstxout = 1000 ; every 2 ps
pull_nstfout = 100 ; every 0.1 ps
Any help or advice would be much appreciated.
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