[gmx-users] Regarding density calculation

Dilip H N cy16f01.dilip at nitk.edu.in
Tue Oct 10 08:10:42 CEST 2017

I have ran a  simulation of 1Gly+255 molecules of water, with my initial
box length being 2.10 nm, and after npt simulation, my final box length (in
the npt.gro file) is 2.090 nm.
For calculating the total density of the system, i used gmx energy command
gmx energy -f npt.edr -o density.xvg, and entered 22 followed by 0. I have
got the density of the system as 987.23 kg/m^-3.

1] But my question is that how do i know this is the actual density of my
simulation system..?? how can i compare this with the experimental

2] In Justin's lysozyme tutorials, in step seven, npt equilibration, it
states that the density of the system is 1006 kg/m^-3, which is close to
the experimental density value of 997.1 kg/m^-3 and the expected density of
tip3p model is 1002kg/m^-3.
How is the experimental density values calculated? where can the values be

3] How do i know for my system that the density that i have got is correct.
(If i view the final npt.gro in vmd i can still see the voids/gaps/spaces
between the molecules, indicating that the box length must be still reduced
further.. or in other words, how can i compactly arrange the molecules in
my simulation box).

Any suggestions are highly appreciated....

With Best Regards,

Ph.D Student

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