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

[Ming Tang]

Dear Chaban,

Thanks for your explanation, and sorry for the late reply. I didn't notice the error when doing mdrun. For one pull-coordn-groups, we need to define two groups. So my aforementioned code is not correct.  But I still did not find out a way feasible to restrain the COM of the reference group. Can you give me some further suggestions?

Thanks a lot.

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of V.V.Chaban
Sent: Sunday, 5 July 2015 10:46 PM
To: gmx-users
Subject: Re: [gmx-users] restrain COM of a group of atoms

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?
>
> Thanks.
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