[gmx-users] trjorder, what and how does es count (amount solvent atoms or molecules)?

Henri Mone henriMone at gmail.com
Sat Mar 12 16:50:07 CET 2011

Dear Gromacs Users,

I'm using "trjorder" with the following options:

$ trjorder -f systemWithSolv.xtc -n system.atom.ndx -s system.pdb -r
0.35  -nshell system0.35.nshell.xvg

As the first group I select all the atoms of a single TYR residue,
which is part of a larger protein. As the second group I select all
the solvent atoms (TIP3P). For a radius of 3.5 A I observe in most
frames the number 8, the observations range from 0 to even 20. What
does this number mean exactly?
For TIP3P the OH2-H1 and OH2-H2 distance is approx. 1A and the H1 and
H2 distance is approx. 1.6A.  This gives a "volume" of 4.2A^3 for
TIP3P. A sphere of 3.5A would have a volume of 14.6A^3. As a first
order approximation this would suggest for non buried TYR residue
about 3 to 4 TIP3P molecules which could fit in this sphere. This
differs from the number 8 which trjorder measures.

My questions are:
1. What does trajorder count? Does it count the number of solvent
atoms or of solvent molecules?
2. How does trajorder count? If trajorder counts the amount of
molecules. Is it sufficient that a single atom of the molecules is in
the sphere to be included in the counting or must all atoms of the
molecule be in the sphere to be included in the counting?


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