Hello, I found out where my mistake. pull_dim is Y Y Y and not N N Y. Bests eef _______________________________________ 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/
On 11 April 2012 10:28, Eudes Fileti <fil...@gmail.com> wrote: > 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 > connecting > the two molecules are not remained on the main axis of the box (z). Then I > realized > 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 > with > 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? > Bests > eef > _______________________________________ > 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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