[gmx-users] g_mindist - reg

[Justin Lemkul]

On 9/3/12 2:04 AM, Raj wrote:
> 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
>
>

If the index groups contain hydrophobic atoms, then yes.  If they contain other 
atoms, then no.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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