[gmx-users] restrain COM of a group of atoms
vvchaban at gmail.com
Sun Jul 5 14:46:54 CEST 2015
I do now know what authors meant. However, the COM-COM pulling implies
that one group is restrained and another group moves relative to it.
So, the COM of the reference group is already fixed in the pull code.
On Sun, Jul 5, 2015 at 4:02 AM, Ming Tang <qut20181127 at gmail.com> wrote:
> 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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