[gmx-users] g_dist

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 9 13:11:12 CEST 2008

minnale wrote:
> Hi all,
>   I want to calculate distance of protein residues by using g_dist, now 
> I have doubt that
> 1.Is it possible to calculate distance for more than two residues of two 
> comparable systems?

g_dist calculates a simple center-of-mass distance between two points.  What 
kind of distance are you trying to calculate that involves more than two points?

> 2. which type of group select for generating index file?

That depends on what you want to analyze.  If you select the whole residue, its 
center of mass will be used in the calculation.  If you are more interested in 
specific functional groups interacting, perhaps you will want only those 
functional groups in the index file (or use g_mindist for a minimum distance 
between the residues).


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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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