Naser, Md Abu wrote:
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.
you can compute center of mass position of groups (g_traj) or shortest
distance between groups (g_mindist)
With 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
-----Original Message-----
From: [EMAIL PROTECTED] 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 <[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
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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