[gmx-users] Re: Pull code: separating molecules. distance and direction (SOLVED)
fileti at gmail.com
Fri Apr 13 14:18:51 CEST 2012
Hello, I found out where my mistake.
pull_dim is Y Y Y and not N N Y.
Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
Tel.: (12) 3309-9573
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
> 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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