VMD-L Mailing List

From: David Wedner (wedner.david_at_yahoo.com)
Date: Tue Nov 16 2010 - 13:24:05 CST

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/
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