[gmx-users] g_mindist - reg

[Raj]

hi all,

I would like to measure the hydrophobic interaction of the ligand against
the protein during the simulation . From the forum I learnt g_mindist will
be the better tool. But when i  used the command  g_mindist -f traj.xtc -s
topol.tpr -n index.ndx -on numcont.xvg -group and selected protein as group1
and ligand as group 2 i get the result like this

g_mindist -f traj.xtc -s pull.tpr -n index.ndx -on numcont.xvg -group
#
# g_mindist is part of G R O M A C S:
#
# Good ROcking Metal Altar for Chronical Sinners
#
@    title "Number of Contacts < 0.6 nm"
@    xaxis  label "Time (ps)"
@    yaxis  label "Number"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Protein-UNK"
0.000000e+00        21
1.000000e+00        21
2.000000e+00        21
3.000000e+00        21
4.000000e+00        21
5.000000e+00        21
6.000000e+00        21
7.000000e+00        21
8.000000e+00        21
9.000000e+00        21
1.000000e+01        21
1.100000e+01        21
1.200000e+01        21
1.300000e+01        21
1.400000e+01        21
1.500000e+01        21
1.600000e+01        21
1.700000e+01        21
1.800000e+01        21
1.900000e+01        21
2.000000e+01        21
2.100000e+01        21
2.200000e+01        21
2.300000e+01        21
2.400000e+01        21
2.500000e+01        21
2.600000e+01        21
2.700000e+01        21
2.800000e+01        21
2.900000e+01        21
3.000000e+01        21
3.100000e+01        21
3.200000e+01        21
3.300000e+01        21
3.400000e+01        21
3.500000e+01        21
3.600000e+01        21
3.700000e+01        21
3.800000e+01        21
3.900000e+01        21
4.000000e+01        21
4.100000e+01        21
4.200000e+01        21
4.300000e+01        21
4.400000e+01        21
4.500000e+01        21
4.600000e+01        21
4.700000e+01        21
4.800000e+01        21
4.900000e+01        21
5.000000e+01        21
5.100000e+01        21
5.200000e+01        21
5.300000e+01        21


I would like to know what ever the data I've obtained is the number of
hydrophobic interaction between the ligand and protein or I am wrong
somewhere. Please help me. Thanks in advance
  



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