VMD-L Mailing List

From: David Wedner (wedner.david_at_yahoo.com)
Date: Wed Nov 17 2010 - 18:40:22 CST

Thanks John and Eddi
you are right
Eddi's suggestion is solving the problem
I did not use it correctly first
Thank you very much

________________________________
From: John Stone <johns_at_ks.uiuc.edu>
To: David Wedner <wedner.david_at_yahoo.com>
Cc: eschrein_at_ks.uiuc.edu; vmd-l_at_ks.uiuc.edu
Sent: Wed, November 17, 2010 12:33:36 AM
Subject: Re: vmd-l: How to Measure Radius of gyration

David,
  In case you didn't catch Eddi's meaning, I think what Eddi was trying
to suggest (by implication) is that you 'unwrap' your PBC trajectory
so the atoms no longer cross PBC boundaries over the course of the
trajectory, and then re-do the rgyr calculations.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 16, 2010 at 11:24:05AM -0800, David Wedner wrote:
> Hi VMD users and thanks Eduard for your reply,
>
> I refereed to the link but I am not able to find the solution of my
> problem
> again my problem is that the cluster that I want to calculate its radius
> of gyration is sometimes broken due to the pbc
> how can I get these molecules together?
> a sample script will be great
> Thanks
>
> David
>
> ----------------------------------------------------------------------
>
> From: Eduard Schreiner <eduard.schreiner_at_gmail.com>
> To: David Wedner <wedner.david_at_yahoo.com>
> Cc: vmd-l_at_ks.uiuc.edu
> Sent: Mon, November 15, 2010 2:47:16 PM
> Subject: Re: vmd-l: Measure Radius of gyration
> Hi David,
>
> you may want to take a look into
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
>
> check also for related questions on the list, it was discussed here a lot.
>
> eddi
>
> On Mon, Nov 15, 2010 at 12:31 PM, David Wedner <wedner.david_at_yahoo.com>
> wrote:
> > Hi,
> > I want to measure the radius of gyration of some methane molecules in a
> > cubic water box
> > the problem is that due to the applied periodic boundary conditions some
> > molecules are transformed to the other side of the box
> >
> > how to transfer these molecules back to their parent position so that I
> have
> > all molecules together ?
> >
> > Thanks
> >
> > David
> >
> >
> >
>
> --
> --
>
>
>=============================================================================
> Eduard Schreiner
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
> Phone: 217-244-4361
> Fax: 217-244-6078
> http://www.ks.uiuc.edu/~eschrein/
>
>============================================================================= 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078