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 <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED]
Phone: +44(0)1314518265
Fax : +44(0) 131 451 3009
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
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