Finding either moles [mol] or mass [kg] of protein dissolved in water

User discussions
1

GROMACS version: 2020
GROMACS modification: Yes/No

Hello, I have a simple protein in water system. Which command should I use to find out the number of moles of the protein (or alternatively mass) in the system I have? Thanks in advance.

2

You can calculate the mass by calculating the density profile of the protein with gmx density, then integrate the profile over your box. Or by reading the protein structure and add atom masses using a script.

3

gmx editconf will report the mass of the system. So you can do a dummy operation like gmx editconf -f conf.gro -o tmp.gro and it will print the mass to the terminal.

The number of moles is easier. If there’s one protein molecule then you have (1/6.022 x 1023) moles in the system.