Calculation of the water inside of protein during trajectory

From: James Starlight (
Date: Tue Feb 03 2015 - 09:51:07 CST

Dear NAMD and VMD users!

I'm looking for the possibility to calculate number of the water molecules
detected within the protein (here I difene area of interests as the resname
MOL) during molecular dynamic simulation (and it will be better to obtain
some graph as well). I've tried to do it using this simple script

[atomselect 0 "water and same residue as within 3 of resname MOL" frame
now] num
but it didn't produce any results

alsobelow script found in the VMD web also didn't work in my case.
Although the visualisation was clearly detected water only on several
snapshots- it's resulted in the saving of each snapshots from trajectory:
set sel [atomselect top "water and same residue as (within 2 of resname
set n [molinfo top get numframes]
for { set i 0 } { $i < $n } { incr i } {
  $sel frame $i
  $sel update
  $sel writepdb ./test/water_$i.pdb

I would be very thankful for any ideas,


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