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: [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.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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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.
[EMAIL PROTECTED]       [EMAIL PROTECTED]   http://folding.bmc.uu.se
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