[gmx-users] wrong distances with g_dist

[lloyd riggs]

Dear Dmytro Kovalskyy,

The ARG CZ is at the end (tip of the ARG), what does the distances look like over time?  A floppy long amino acid?  And your actual distance calculation?  Is it from a graphics/pdb file, or how is it measured?

Stephan

-------- Original-Nachricht --------
> Datum: Tue, 26 Jun 2012 16:14:31 -0500
> Von: Dmytro Kovalskyy <kovalskyy at uthscsa.edu>
> An: gmx-users at gromacs.org
> Betreff: [gmx-users] wrong distances with g_dist

> Hi,
> 
> I try to calculate distance between two atoms with g_dist. Somewhat I get 
> distance lower than actual.
> Here there are coordinates of the two atoms (PDB format)
>  
> ATOM    702  CZ  ARG X  45       5.930   9.230  41.740  0.00  0.00
> ATOM   2751  CA  PHE X 177      41.710  45.000  27.180  0.00  0.00
> 
> And the distance I get from g_dist is 4.6260725 nm while the actual is
> 5.265 
> nm.
> 
> What the problem can be?
> 
> Dmytro
> 
> 
> 
> 
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