[gmx-users] How to count the number of waters in the first hydration shell of a macromolecule

[chris.neale at utoronto.ca]

Dear users:

I believe that the easiest way to calculate the number of water  
molecules in the first hydration shell of a macromolecule or molecular  
cluster is as follows.

## Set your cutoff as determined from g_rdf
DIST=0.435

## Calculate the data using g_mindist -respertime
echo -e "SOL_OW\nProtein_heavy\n" | g_mindist  -s my.tpr -f my.xtc -n  
my.ndx -d ${DIST} -respertime -od od.xvg -or or.xvg

## Extract the desired numerical values from or.xvg
grep -v '[#|@|S]' or.xvg |awk  
'{s=0;for(i=2;i<=NF;i++)if($i<'${DIST}')s++;print $1,s}' >  
water_count.dat

This method does not work with gromacs 4.0.x. I am using g_mindist  
from version 4.5.3 here. From my tests, I get the correct values when  
using g_mindist version 4.5.3 and a .tpr and .xtc from gromacs version  
4.0.7.

This is a final comment from the original post titled "interfacial  
water molecules"
http://lists.gromacs.org/pipermail/gmx-users/2010-December/056912.html

I don't believe that there is currently a flag to output this number  
directly from g_mindist.

Chris.