[gmx-users] distance measurement

[Naser, Md Abu]

Hi Tsjerk,

Thanks for your response. I mean edge of decane-water interface. I have a protein solvated in water and I want to measure distance between the interface and protein over time.

With regards, 

Abu Naser 

School Of Life Sciences 
Heriot-Watt University 
Edinburgh EH14 4AS 
Email: mn2 at hw.ac.uk
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 


 



-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Tsjerk Wassenaar
Sent: Thu 30/03/2006 7:37 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] distance measurement
 
Hi Abu,

What edge? There are no edges when using periodic boundary conditions. Is
there any particular reason why you would need such a measurement? If you
want the "distance to the wall", you will need to calculate the minimal
distance between periodic images (g_mindist -pi) and take half of that. You
could ofcourse take the maximal z-coordinate and subtract it from the third
number of the last line of the .gro file (which gives the z component of the
third box vector).

Cheers,

Tsjerk

On 3/30/06, Naser, Md Abu <mn2 at hw.ac.uk> wrote:
>
> Hi All,
>
> Is there anyway I can measure distance between protein and edge of a box
> in z direction?
>
> Regards,
>
> Abu Naser
>
> School Of Life Sciences
> Heriot-Watt University
> Edinburgh EH14 4AS
> Email: mn2 at hw.ac.uk
> Phone: +44(0)1314518265
> Fax : +44(0) 131 451 3009
>
>
>
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>


--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060330/bfe909d9/attachment.html>