[gmx-users] test on g_density

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Feb 23 13:53:28 CET 2011

Could it be this:


I've posted a few times on the fact that this tool is broken for  
constant pressure simulations.

I'm not sure why both even and odd would be under the overall average,  
but it seems possible.


-- original message --

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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