[gmx-users] Re: Pull code: separating molecules. distance and direction (SOLVED)

[Eudes Fileti]

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 <fileti at 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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