[gmx-users] Water molecule in the first hydration shell

[Justin Lemkul]

On 1/20/19 1:01 AM, ISHRAT JAHAN wrote:
> Dear all,
> I want to calculate the number of water molecule within 5 A of protein
> throughout the trajectory. I have calculated it using the command-
>    gmx select -n water.ndx -select 'group "water" and within 0.5 of com of
> group "Protein" -os out.xvg  -f  pbc.xtc -s  200ns.tpr -b 110 -tu ns

This selection will give you waters within 5 A of the center-of-mass of 
the protein, which will not encompass the hydration shell.

-Justin

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Justin A. Lemkul, Ph.D.
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