[gmx-users] Pull code: separating molecules. distance and direction
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
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
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_pbcatom0 = 0
pull_group1 = mol_1
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
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