[gmx-users] test on g_density

Tue Feb 22 20:29:42 CET 2011

Hi all.

I've noticed an unexpected behaviour using g_density. I have a  
trajectory (with time step 2) and it is split into two subsets (using  
trjconv) with, lets say, even and odd steps respectively. According  
the the algorithm I expected that the density obtained with the  
original trajectory would be the average of the density with each  
generated trajectory. However, that was not the case, and for each  
slice, while density calculated from the subsets was practically the  
same, the density calculated with the original was different (greater  
or lower). My system is a membrane, the original trajectory is 50ns  
long (25001 steps) and I calculate the density along the bilayer  
normal (z). I am using GROMACS4.5.3 and a I've issued the following  

*To get the subsets:
trjconv -f bilayer.xtc -s bilayer.trp -o bilayer_odd -dt 4
trjconv -f bilayer.xtc -s bilayer.trp -o bilayer_even -dt 4 -b 2

The generated trajectories have 12501 and 12500 steps respectively.

*To calculate the densities:
g_density -f bilayer.xtc -s bilayer.tpr -o dens_all
g_density -f bilayer_odd.xtc -s bilayer.tpr -o dens_odd
g_density -f bilayer_even.xtc -s bilayer.tpr -o dens_even

The result is attached. dens_odd and dens_even are very similar, but  
surprisingly (at least for me), dens_all is different (it actually  
integrates more atoms than the other two).

I haven't seen anything in the code that could explain that result  
(maybe when removing pbc??). Is it a bug or a mistake from me?

Thank you!

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