<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<META NAME="Generator" CONTENT="MS Exchange Server version 6.5.6944.0">
<TITLE>RE: [gmx-users] distance measurement</TITLE>
</HEAD>
<BODY>
<!-- Converted from text/plain format -->
<P><FONT SIZE=2>Hi Tsjerk,<BR>
<BR>
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.<BR>
<BR>
With regards,<BR>
<BR>
Abu Naser<BR>
<BR>
School Of Life Sciences<BR>
Heriot-Watt University<BR>
Edinburgh EH14 4AS<BR>
Email: mn2@hw.ac.uk<BR>
Phone: +44(0)1314518265<BR>
Fax : +44(0) 131 451 3009<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org on behalf of Tsjerk Wassenaar<BR>
Sent: Thu 30/03/2006 7:37 PM<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] distance measurement<BR>
<BR>
Hi Abu,<BR>
<BR>
What edge? There are no edges when using periodic boundary conditions. Is<BR>
there any particular reason why you would need such a measurement? If you<BR>
want the "distance to the wall", you will need to calculate the minimal<BR>
distance between periodic images (g_mindist -pi) and take half of that. You<BR>
could ofcourse take the maximal z-coordinate and subtract it from the third<BR>
number of the last line of the .gro file (which gives the z component of the<BR>
third box vector).<BR>
<BR>
Cheers,<BR>
<BR>
Tsjerk<BR>
<BR>
On 3/30/06, Naser, Md Abu <mn2@hw.ac.uk> wrote:<BR>
><BR>
> Hi All,<BR>
><BR>
> Is there anyway I can measure distance between protein and edge of a box<BR>
> in z direction?<BR>
><BR>
> Regards,<BR>
><BR>
> Abu Naser<BR>
><BR>
> School Of Life Sciences<BR>
> Heriot-Watt University<BR>
> Edinburgh EH14 4AS<BR>
> Email: mn2@hw.ac.uk<BR>
> Phone: +44(0)1314518265<BR>
> Fax : +44(0) 131 451 3009<BR>
><BR>
><BR>
><BR>
><BR>
><BR>
> _______________________________________________<BR>
> gmx-users mailing list gmx-users@gromacs.org<BR>
> <A HREF="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>
> Please don't post (un)subscribe requests to the list. Use the<BR>
> www interface or send it to gmx-users-request@gromacs.org.<BR>
> Can't post? Read <A HREF="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR>
><BR>
><BR>
<BR>
<BR>
--<BR>
<BR>
Tsjerk A. Wassenaar, M.Sc.<BR>
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<BR>
Dept. of Biophysical Chemistry<BR>
University of Groningen<BR>
Nijenborgh 4<BR>
9747AG Groningen, The Netherlands<BR>
+31 50 363 4336<BR>
<BR>
<BR>
</FONT>
</P>
</BODY>
</HTML>