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: [EMAIL PROTECTED]
Phone: +44(0)1314518265
Fax : +44(0) 131 451 3009
-----Original Message-----
From: [EMAIL PROTECTED] 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" <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED]
Phone: +44(0)1314518265
Fax : +44(0) 131 451 3009
-----Original Message-----
From: [EMAIL PROTECTED] 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: [EMAIL PROTECTED]
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.
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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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