[gmx-users] fix COM of a group

[Ming Tang]

Dear Tsjerk,

Yes, you are right. I want to fix the COM of the reference group (one end of a triple helix), and pull the other end. I tried to freeze the reference group, but found this setting restricted the unfolding process of my triple helix. That's why I want to find a way to fix the COM only.

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 11:18 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] fix COM of a group

Hi Ming Tang,

You didn't tell you were pulling... That's a totally different matter. I guess you want to use two pull groups and pull one with respect to the other.

Cheers,

Tsjerk

On Wed, Jun 3, 2015 at 11:20 AM, Ming Tang <m21.tang at qut.edu.au> wrote:

> 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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Tsjerk A. Wassenaar, Ph.D.
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