[gmx-users] positions and velocities of COM of whole water molecules instead of those of individual atoms?

[bohumir]

>> Dear GROMACS Masters,
>>
>> is there a trick to obtain coordinates and velocities of center of
>> mass of each water molecule?
>>
>
> Have a look at g_traj, although to analyze each molecule separately could
> take many iterations with specific index groups.
>
g_traj can really do it (for coordinates), thanks!

g_traj with -mol option was what I needed. It is documented in the
third sentence
of the DESCRIPTION section of g_traj manual...

   "When  -mol is set, the numbers in the index file are interpreted as molecule
    numbers and the same procedure as with -com is used for each molecule."

-Bohumir