[gmx-users] Pull code: separating molecules. distance and direction

Eudes Fileti fileti at gmail.com
Wed Apr 11 15:28:12 CEST 2012

Hello everybody, I have used pull code to separate two molecules in water.
The idea is to generate initial configurations for umbrella sampling.
Initially I tried to use pull_geometry=distance. I noticed that the vector
the two molecules are not remained on the main axis of the box (z). Then I
that using pull_geometry=direction (with pull_vec1= 0 0 1) I could keep
this distance
on the z axis. However, the result of the pulling was exactly the same as
pull_geometry=distance, ie, as the molecule moves away from the reference
molecule the
distance of separation does not remain on the z axis, as I wish.

The protocol used was as follows:
pull                     = umbrella
pull_geometry            = direction
pull_dim                 = N N Y
pull_ngroups             = 1
pull_group0              = mol_0
pull_weights0            =
pull_pbcatom0            = 0
pull_group1              = mol_1
pull_weights1            =
pull_pbcatom1            = 0
pull_vec1                = 0.0 0.0 1.0
pull_init1               = 0.0
pull_rate1               = 0.01
pull_k1                  = 1000

Someone could direct me to where I am wrong?
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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