[gmx-users] g_dist

[Naser, Md Abu]

Hi XAvier,

Yes, now it makes sense.

Thank you very much for making it clear.


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 8:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_dist
 

The output of g_dist gives:

time distance   DeltaX DeltaY DeltaZ

distance = sqrt(DeltaX**2+DeltaY**2+DeltaZ**2)

DeltaX, Y or Z are the differences of the atomic (COM)
positions in each direction. A negative value simply means
that one of the atoms (COM) has a value larger than the
other one in the corresponding direction.

The negative value is not a distance yet! Just the
difference between the two atoms (COM) positions
on one direction.

Would that make sense?

> 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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>> 
>> 
>> -- 
>> 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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-----------------------------------------------------
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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