[gmx-users] hydrophobic contacts

Turgay Cakmak turgaycakmak34 at gmail.com
Wed Jun 6 17:46:16 CEST 2012

Hi All,

To be able to get information about the  hydrophobic contacts, I prepared
index.ndx which includes 2 groups of atoms that belong to hydrophobic
residues of my system. Then, I used the command

“g_dist -f traj.xtc -s topol.tpr -n index.ndx -dist 0.4 -lt -o
lifetime.xvg” .

which gave  the “Number of contacts versus time” graph. But, number of
contact axis contains numbers from 0 to 0.5 (can the number of contact be a
non-integer?) and the time axis is given between 0 and 500 ps  (But, I have
totally done a 70 ns simulation).

This is the first time I am looking for such interactions.  I could not
understand these numbers

Any help would be appreciated.

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