[gmx-users] g_dist

[David van der Spoel]

Naser, Md Abu wrote:
> 
> 
> Hi David,
> 
> Yes, it should be a vector as it is a difference between the center of 
> mass of two groups in
> x,y, and z directions. Then, negative means an opposite direction. Is 
> that right?

g_dist -h:

g_dist can calculate the distance between the centers of mass of two 
groups of atoms as a function of time. The total distance and its x, y 
and z components are plotted.

if you reverse order of the groups the numbers will change sign.

> 
> 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 David van der Spoel
> Sent: Tue 25/09/2007 9:42 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] g_dist
> 
> Naser, Md Abu wrote:
>  >
>  >
>  > Hi all user,
>  >
>  > I have just calculated a distance between backbone and side chain of the
>  > same protein. I get
>  > negative distance along x and y direction. What dose negative 
> distance mean?
>  >
> please be more specific. is that a vector?
> 
>  > Thanks in advance.
>  >
>  >
>  > 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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> 
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se