[gmx-users] distance measurement

[David van der Spoel]

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: 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
>  >
>  >
>  >
>  >
>  >
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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.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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