[gmx-users] Center of mass distance

[X.Periole]

On Thu, 4 May 2006 23:48:28 -0400 (EDT)
  "YOLANDA SMALL" <yas102 at psu.edu> wrote:
> Hello,
> 
> I would like to determine the percentage of water 
>occupation in a protein region
> by calculating the distance between the center of mass 
>of a group of atoms and
> the solvent.  Does anyone know which gromacs tools can 
>provide an estimate of
> this information?  By the way my trajectory is in xtc 
>format.
> 

you could try g_mindist, which gives the minimum distance
between 2 groups and counts the number of contacts (water)
within a given distance from a group (protein).

you could also see if trjorder coudl help. It orders a 
group
(solvent) by distance to a give grou (protein).

XAvier