Follow the following articles

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032036

Article Evidence of Water Molecules—A Statistical Evaluation of Wate...

https://academic.oup.com/peds/article/24/10/777/1440813

These articles may be helpful. Thanks

You can use Tcl script below in VMD; it will show the water molecules within 3 A of protein.

mol new *.psf

mol addfile *.dcd

set frames [molinfo top get numframes]

set fp [open "waters.txt" w]

set protein "protein"

for {set i 0} {$i < $frames} {incr i} {

                puts "Frame: $i"

                set a [atomselect top "(water within 3 of ($protein) )" frame $i]

                set num [$a num]

                puts $fp "$i $num"

                $a delete

}

close $fp

Thanks for suggestion.

Can i use gmx trjorder command with -nshell flag for calculating no. of water molecule at particular distance from protein surface?

You can take the radial distribution function using gmx rdf command. Take the rdf of water around the protein.

I recommend you to use gmx select with this command line

gmx select -f -s -n -of -ofpdb -selrpos atom -seltype res_com -select 'group X and within 0.4 of group Y'

X means a group with protein atoms

Y means a group with water atoms

this will tell you wich water molecules are 0.4 nm of the protein and how often are they . In the occupancy.xvg you should be able to see results

Also you can use gmx mindist

https://www.researchgate.net/deref/http%3A%2F%2Fjournals.plos.org%2Fplosone%2Farticle%3Fid%3D10.1371%2Fjournal.pone.0032036

Claudia Mejías Márquez ,

Hi, I want to define a selection i.e., 5Ang volume around a certain group of residues (from different chains Asp263 (chain B) Asp366 (chain C ) that make your binding site --- Within this selection I want count number of waters molecules along the trajectory (its a membrane trajectory with water and lipid POPC).

Looking forward to hear from you.

Sincere Regards

Budheswar