[gmx-users] trjorder

[Nidhi Katyal]

Dear all
I would like to know the number of oxygen atoms of my co-solvent
molecules which are around 0.3nm of the protein in the last few ns. I
have read the manual and found that trjorder could serve the purpose.
So i have first created index file containing all the oxygen atoms of
my co-solvent molecules. Then I have used the following command:
trjorder -f *.xtc -s *.tpr -b 18000 -e 20000 -nshell nshell.xvg -na 1
Here I have used na as 1 since I am interested in number of atoms
instead of molecules (although one cosolvent molecule consists of 11
oxygen atoms).
Please guide me if I am proceeding in the right direction and if I am
wrong what na value should I give to serve the required purpose.
Thanks in advance.