[gmx-users] distance measurement
Naser, Md Abu
mn2 at hw.ac.uk
Thu Mar 30 21:48:46 CEST 2006
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.
School Of Life Sciences
Edinburgh EH14 4AS
Email: mn2 at hw.ac.uk
Fax : +44(0) 131 451 3009
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
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).
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?
> 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
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
9747AG Groningen, The Netherlands
+31 50 363 4336
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