[gmx-users] problems with g_dist

[Luca Monticelli]

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?

thanks a lot

luca

-- 
____________________________________________________

Luca Monticelli
Centre for bio-molecular 
Interdisciplinary Studies
and Industrial applications
University of Milan, Italy
Istituto di Chimica del Riconoscimento 
Molecolare
C.N.R., Milano, Italia
e-mail: luca.monticelli at unimi.it
phone: +39 02 2850 0031
fax:   +39 02 2850 0036
____________________________________________________