[gmx-users] Pull to separate dimer
fabracht1 at gmail.com
Sat Aug 22 04:44:00 CEST 2009
I am trying to learn how to use the pull code to separate a dimer. I have
read gromacs 4 manual and a tutorial I found on CSC, but it seems I still
haven´t got the knack.
My system is consisted of a dimer inserted into a membrane lipid bilayer. I
have included the following lines into my mdp parameter file.
pull = umbrella
pull-geometry = direction
pull_dim = Y N N
pull_nstxout = 10
pull_nstfout = 1
pull_ngroups = 1
pull_group0 = DPPC
pull_group1 = r_31-60
pull_vec1 = 1 0 0
pull_init1 = 0.0
pull_rate1 = 0
pull_k1 = 1000
Since I am trying to separate the two structures I thought about using the
DPPC membrane as a reference structure for the pull, since my attemps with
the monomer as a reference struture went with nothing happening whatsoever.
Is it correct to use such a long series of aminoacids as a pull reference,
i.e., gromacs will understand that tha pull should be in the center of mass,
right? What does the manual mean with "grompp normalizes the vector"? Is
this how I should procede to separate my dimer?
Thank you in advance
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