[gmx-users] Re: how to remove periodicity when using g_rmsd

[Mauricio Pablo Sica]

... and, in the case that you have several not-covalently-bound chains, 
use a 'topol.tpr' corresponding to a simulation beginning with all the 
chains within the same box. (I think Tsjerk suggested that to me several 
months ago)

Mauricio Sica

> 
> Hi Tangj Jioawei, Erik.
> 
> This is due to periodic boundary conditions. Make sure your molecules
> stay together (clustered/nojump) before determining the rmsd. Use
> trjconv...
> 
> Tsjerk
> 
> On 9/27/07, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> > My first guess, without knowing how you used g_rms, is that the larde
> rmsd
> > for certain subunits is due to inadequate roto-translational fit
> prior to
> > rmsd-calculation. Does that help? If not, please be more explicit
> about what
> > you aim to do and what you have done.
> >
> > /Erik
> >
> >
> > 27 sep 2007 kl. 11.29 skrev TANG JIAOWEI:
> > Dear all,
> > I am studying on a big protein with 16 subunits and when i used
> g_rmsd to
> > one subunit of the protein, the result seems strange that the
> structure of
> > the subunit changes much but it should not.. I searched the mailing
> list and
> > it may be caused by the periodic thing. Could you tell me how to
> remove the
> > periodic thing in detail before i use g_rmsd.
> >
> > Thank you
> >
> > Tang jiaowei