[gmx-users] Pull to separate dimer

Ragnarok sdf 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
Fabrício Bracht
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