[gmx-users] g_dist

[Naser, Md Abu]

hi XAvier,

Thanks for your response. 
It was a question more of about how you would interpret the
negative values(distance) in a particular component.

With thanks,

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 Xavier Periole
Sent: Tue 25/09/2007 10:13 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_dist
 
On Tue, 25 Sep 2007 10:03:30 +0100
  "Naser, Md Abu" <mn2 at hw.ac.uk> 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 gives the distance and the component in each direction.
The components been the difference between the atomic (or COM)
positions there is no problem in having a negative value.

> 
> 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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>> 
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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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-----------------------------------------------------
XAvier Periole - PhD

1- Institute of Molecular Assemblies
      City University of New York - USA
2- Molecular Dynamics-Group
      University of Groningen - The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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