[gmx-users] how to know solvent molecule number

Vytautas Rakeviius vytautas1987 at yahoo.com
Wed Apr 5 15:45:30 CEST 2017

head -n 2 obj.gro | tail -n 1Print number of molecules in obj.gro file. Solvate then do same on new file:
head -n 2 obj_solv.gro | tail -n 1All you need is difference.

    On Wednesday, April 5, 2017 4:13 PM, Chintan Bhagat <cbb.chintan at gmail.com> wrote:


I want to do stimulation of my protein in solvent, ethanolamine (different
I have made box of 1 nm and then using command
"gmx solvate -cp 1AKI_newbox.gro -cs ethanolamine.gro -o 1AKI_solv.gro -p
As per my knowledge, i solvated my protein in ethanolamine.
Now I want to know the number of ethanolamine molecule present in box. Then
I looked in to *.top* file but no information is availble in the file (SOL).
(As per intruction, program is only hard-coded to update the topology in
the case of water).
I found increase in number of molecules from 7200 to 128004 in
/home/lab1/Desktop/md2/1AKI_processed.gro.gro and 1AKI_solv.gro,
respectively. It means something is inserted in box (must be
ethanolamine!!!!!-my guess)
How can i know number of ethanolamine molecules?

for reference please find attched files.

Thanking you in advance.
Chintan Bhagat
Research scholar,
Veer Narmad South Gujarat University,
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