[gmx-users] Center of mass distance

X.Periole X.Periole at rug.nl
Fri May 5 08:53:07 CEST 2006

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 

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 
(solvent) by distance to a give grou (protein).


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