[gmx-users] problems with g_dist

[Alessandra Villa]

Hi Luca


> Hi,
> 
> I would like to use the g_dist tool to 
> calculate distances between atoms during 
> my simulation (to be compared with NMR 
> distances); unfortunately, it looks like 
> g_dist does not work on hydrogens nor 
> dummy atoms (using the option -dummy 
> aromatics, CD* in Phe, Tyr, His and all 
> aromatic carbons in Trp are dummies!). I 
> guess this is because g_dist calculates 
> distances between centers of mass, right?
> Is there any (simple) way to calculate 
> distances between zero-mass atoms?
> 

You could use 
g_bond -d 
to calculate the distance between 2 atoms
defining in the index file :
{ a b } 
atomA atomB

or you could use g_mindist if you are interested in the minumun distance
between two group 

regards

Alessandra