Hi
I pulled an ion to move along the axial direction in a nanotube by using SMD
simulation, with the version of Gromacs-4.0.7. For some cases, the simulations
stopped without any errors. The simulation could properly run, but it did not
run to the end. The following is the pulling code in my .mdp file.
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = constraint
; Pull geometry: distance, direction, cylinder or position
pull_geometry = direction
; Select components for the pull vector. default: Y Y Y
pull_dim = N N Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1 = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0 = 1.5
pull_constr_tol = 1e-06
pull_start = no
pull_nstxout = 10
pull_nstfout = 10
; Number of pull groups
pull_ngroups = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)
pull_group0 =
pull_weights0 =
pull_pbcatom0 = 0
pull_group1 = Na
pull_weights1 =
pull_pbcatom1 = 0
pull_vec1 = 0.0 0.0 1.0
pull_init1 = 10.500
pull_rate1 = 0.0563104
pull_k1 =
pull_kB1 =
Is there any parameters in the pulling code setted with improper values? Anys
suggestions or answers are appreciated.
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