[gmx-users] Calculating density of a particular run segment

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 17 06:39:10 CET 2009

Lum Nforbi wrote:
> Hello all,
>    I have tried this command line to find the density of a system at 
> particular time interval:

If your volume is changing, system density is already reported in the 
simulation .edr file. Use g_energy to get it. grompp probably reported 
the initial density.

> g_density -f traj.xtc -s topol.tpr -b 1228 -e 1328 -o density.xvg,
> but I keep having the result to the full mdrun. 

What do you mean by this last sentence?

> The plot of the density 
> vs box dimension is also obtained via xmgrace. I need to plot this 
> density in terms of time. Is it possible to do so?

Yes. As above, or using your command if your .xtc has saved coordinates 
for the whole system between those times.

> Also, I need help 
> with help with adjusting the above command line so that I can find the 
> density of only one segment of the run.

It should work as above.


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