[gmx-users] Distance of pull group is larger than half the box size

[Eudes Fileti]

Hello guys, I have tried to calculate the PMF for a dimer in a
rectangular box of dimensions 3 x 3 x 7. However, the simulation
stops when the COM separation is above 1.49 (ie half
of the smallest dimension of the box. Since I am pulling along
the Z axis at a distance that would be up to 3.5 nm.

I've tried both pull_geometry, distance and direction, to try to get
around this, but I have not been successful.

Do I have to use the dimensions of the box as twice the COM
distance (in my case: 5 x 5 x 5; to give me r_max = 2.5nm)?

Some of you could give me a hand?


DIRECTION
pull                     = umbrella
pull_geometry            = direction
pull_dim                 = Y Y Y
pull_group0              = mol_0
pull_group1              = mol_1
pull_rate1               = 0.01
pull_vec1                = 0.0 0.0 1.0
pull_k1                  = 3000

DISTANCE
pull                     = umbrella
pull_geometry            = distance
pull_dim                 = Y Y Y
pull_group0              = mol_0
pull_group1              = mol_1
pull_rate1               = 0.01
pull_vec1                = 0.0 0.0 0.0
pull_k1                  = 3000
_______________________________________
Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
Tel.: (12) 3309-9573
Página: sites.google.com/site/fileti/
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