[gmx-users] Regarding density calculation

Mark Abraham mark.j.abraham at gmail.com
Tue Oct 10 13:08:07 CEST 2017


You can only compare to an experimental value by having available the
results of an experiment... obviously you measure density by making a known
composition and measuring its mass and volume.

If you've equilibrated your volume in NPT, there are no voids. Anything you
think is a void is being filled from the other side of the periodic box.


On Tue, Oct 10, 2017 at 8:10 AM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> Hello,
> 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
> as,
> 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
> values..??
> 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
> available..??
> 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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