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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