[gmx-users] constant force pulling

kim2811 kmanibog at iastate.edu
Mon Jul 29 20:42:39 CEST 2013


I am trying to pull/separate a protein dimer by applying constant force in
my SMD. The dimer has dimension 9 x 8 x 5 nm^3, and I'm trying to pull in
the y-direction so I have set the box as 12 x 40 x 8 nm^3. I have also set
my simulation to run for 5 ns. However, after only 251 ps, I got this fatal

  Distance of pull group 1 (3.958423 nm) is larger than 0.49 times the box
size (16.314939)

Can somebody please interpret this error? When I checked the trajectory, the
protein seems to be inside the box or at least the COM of the dimer is near
the center of the box, so the protein approaching near the boundary can't be
the reason for this error. If it can help to clarify, here's my pull code:

; Pull code
pull            = constant_force
pull_geometry   = direction  ; pull in the direction of pull code 
pull_dim        = Y Y Y
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = chain_A  ; C-terminal of Protein 1
pull_group1     = chain_B  ; C-terminal of Protein 2 
pull_k1         = -500      ; kJ mol^-1 nm^-1
pull_vec1       = 0 1 0 

Thank you.

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