On Thu, 4 May 2006 23:48:28 -0400 (EDT)
 "YOLANDA SMALL" <[EMAIL PROTECTED]> 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
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