[gmx-users] fix COM of a group

[Ming Tang]

Dear Tsjerk,

Thanks for your guidance. I add those two command lines you gave in .mdp, but got the following warnings.

WARNING 1 [file dynamic.mdp]:
  Some atoms are not part of any center of mass motion removal group.
  This may lead to artifacts.
  In most cases one should use one group for the whole system.

Number of degrees of freedom in T-Coupling group Protein is 8680.88
Number of degrees of freedom in T-Coupling group non-Protein is 202734.12
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K
Calculated rlist for 1x1 atom pair-list as 1.406 nm, buffer size 0.006 nm
Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm

WARNING 2 [file dynamic.mdp]:
  You are using an absolute reference for pulling, but the rest of the
  system does not have an absolute reference. This will lead to artifacts.

Pull group  natoms  pbc atom  distance at start  reference at t=0
       0         0         0
       1         3      1919      -1.542 nm         -1.542 nm

Can I just ignore them? 
Thanks.

-----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 Tsjerk Wassenaar
Sent: Wednesday, 3 June 2015 5:41 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] fix COM of a group

Hi Ming Tang,

comm_mode = Linear
comm_grps = CA

Cheers,

Tsjerk

On Wed, Jun 3, 2015 at 9:34 AM, Ming Tang <m21.tang at qut.edu.au> wrote:

> Dear all,
>
> Is there any method that can fix the center of mass of a group of 
> atoms? I create a group containing CA atoms of the first residue in 
> each of the three chains, and want to fix its center of mass only 
> without freeze the CA atoms.
>
> Thanks.
> --
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Tsjerk A. Wassenaar, Ph.D.
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