[gmx-users] pulling of a metal

Jon Mujika joni.mujika at ehu.es
Wed Apr 13 18:23:49 CEST 2011

Dear all,

I am trying to pull a metal out of the protein binding pocket following a
cavity in the protein structure. I followed the tutorial, but I find few

1) When the metal leaves the binding pocket, some ligands "follow" the
metal, even that  I restrained the position of protein atoms (force constant
of 1000 or 3000). I would like to keep the protein as it is.

2) The metal does not leave the protein through the cavity. How can I define
this? I can take a water molecule in the cavity as reference, but I do not
how to deal with this.

This is the pull section in the mdp file:

pull            = umbrella
pull_geometry   = distance
pull_dim        = N N Y
pull_start      = yes           ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Protein
pull_group1     = Metal
pull_rate1      = 0.01          ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 3000          ; kJ mol^-1 nm^-2

Thanks in advance for your help

Jon Mujika
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