[gmx-users] Center of mass distance

YOLANDA SMALL yas102 at psu.edu
Fri May 5 16:51:19 CEST 2006

Thanks for the suggestion Xavier.  However, I already tried g_mindist and the
problem is that it does not use the center of mass of the reference group to
calculate the distance to the atoms of the solvent group.  Instead, it computes
all possible distances between pairs of atoms between the groups at a given
time and gives the minimum distance from any of the atoms in the reference
group it finds.

Perhaps if there is a way to input coordinates to represent a dummy atom then
use g_mindist to calculate the distance and number of contacts between the
dummy atom and each solvent atom within the cutoff range that would give me the
estimate that I am looking for.


On Fri, 05 May 2006 08:53:07 +0200, "X.Periole" wrote:

> 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

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