[gmx-users] problems with g_dist

[Anton Feenstra]

Luca Monticelli wrote:

> 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?


Right.

> Is there any (simple) way to calculate distances between zero-mass atoms?


For a "simple" solution: see Alessandra Villa's mail.

An alternative is to make a topology of your system without the dummy
definitions, and to also convert your trajectory to one without dummies
(additional atoms are added for -NH3 / -CH3 groups). The first is
simple: run pdb2gmx again, without -dummy, then run grompp with your
new .top file. The second is also simple: run trjconv on your
trajectory, and supply the original .tpr (with dummies), then select
for output the Protein-M group (that excludes the added atoms). Now
you have a new .xtc (or .trr) and .tpr in which all atoms are defined
as normal atoms with mass etc. (note that the dynamic behavior in the,
obviously, still includes the effects of the dummies). These new files
can be used with g_dist.


--GRoetjes,
Anton