[gmx-users] restrain COM of a group of atoms

Ming Tang qut20181127 at gmail.com
Sun Jul 5 09:02:33 CEST 2015

Dear Gromacs experts and users,

I am here to seek help. I want to use constraint pull method to pull a
filament. My plan is to keep the center of mass of one group "fixed"
through a stiff restraint, say 3×10e5, and pull the other group. I tried to
generate the restraint .itp file and modify the topol ifle, but found that
I can only restrain all of the atoms, not the COM of the group. There are 2
journals, in which the authors said they used this method like this:
To apply uniaxial tension, the center of mass of the N-terminal C − α atoms
of the two chains was fixed by a stiff harmonic spring and referred as the
reference group. they used GROMACS 4.6. I am using version 5.0.4. I tried
to use pull code to achieve this, but failed. My code is like this:

pull                = constraint
pull-geometry       = direction-periodic
pull-start          = yes
pull-ngroups        = 2
pull-ncoords        = 2
pull-coord1-groups  = 1
pull-coord2-groups  = 2
pull-group1-name    = G1
pull-group2-name    = G2
pull-coord1-rate    = 0.0005
pull-coord2-rate    = 0
pull-coord1-k       = 4000
pull-coord2-k       = 300000
pull-coord1-vec     = 1 0 0
pull-coord2-vec     = 1 0 0

using this pull code, I found that only the displacement along Z direction
of  COM of  G1 was 0 during the simulation, and the displacement along both
x direction and y direction changed.

Could anybody give me some guidance?


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