[gmx-users] Protein distance with respect to box walls

[xu zhijun]

Try to use the VMD to directly measure the distance between the protein and box boundary. 
 

     On Tuesday, December 9, 2014 8:16 AM, "Smith, Micholas D." <smithmd at ornl.gov> wrote:
   

 Hi James,

The utility g_mindist lets you measure the minimum distance between a selection and its periodic image, if what you are trying to do is just confirm that your simulation box is large enough to prevent periodic image effects, this is one way to check.

Kind Regards,

Micholas

===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of amin at imtech.res.in <amin at imtech.res.in>
Sent: Monday, December 08, 2014 11:39 PM
To: Gmx users
Subject: Re: [gmx-users] Protein distance with respect to box walls

Dear James,

I think if you load your system in VMD you can measure the dimensions of
protein with something like

set sel [atomselect top "protein"]

measure minmax $sel

Regards.

Amin.

On 2014-12-09 08:55, James Lord wrote:

> Dear Users,
> I have a protein in a box and was wondering to know how to figure out the
> protein distance to the box walls? I can see the box dimensions at the end
> of .gro file but how to know what is (x,y,z) of protein in the box?? any
> comments?
> Cheers
> James


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