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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