[gmx-users] problem in g_density

[Mark Abraham]

On 8/06/2011 9:41 PM, cdalgicdir wrote:
> Hi,
>
> The simulation box consists of layers of cyclohexane and vacuum. 
> Ensemble is NVT.
>
> The density profiles of cyclohexane for 5-10 ns, 10-15 ns and 15-20 ns 
> coincide. However the density profile for 5-20 ns is significantly 
> higher than the ones calculated.
> g_density -n -b 5000 -e 20000
>
> If I calculate the 5-20 ns interval using every 5th frame the density 
> profile resembles that of the 5-10, 10-15, 15-20 ns's.
> g_density -n -b 5000 -e 20000 -dt 5
>
> Attached is the graph of these profiles.
>
> I have tried this in 4.07, 4.5.3 and 4.5.4. The results are similar 
> for all these versions.
>
> I am aware that such inconsistencies may occur with g_density in NPT 
> ensembles. However I am using a NVT ensemble. Is there something am I 
> missing? And more importantly,  how should I decide which one is the 
> correct density?

I'd guess this is an artefact of the fact that the times in the 
trajectory file are not exactly multiples of the time step. That is just 
life - see 
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic. If so, 
one or more of these ranges is probably not computing over the set of 
frames you think it is. Consider using suitable non-integers for -b and 
-e, and avoiding -dt unless you know it will work on the times that 
exist. trjcat -settime can help, also.

Mark