[gmx-users] Density Problem

Mark Abraham Mark.Abraham at anu.edu.au
Sat Apr 25 01:17:23 CEST 2009

Zhang Hui wrote:
> Dear All,
>          I just found that there is a problem when I extract the density
> of water from my Gromacs simulations.
>          When I used g_density to get the water density from .trr
> trajectory file, the density plot looked normal. But when I used trjconv
> to convert the .trr to .gro file, and then used g_density to get the
> water density from .gro trajectory file, there was an unusual
> periodicity in the densities. The density comparison plot is attached.
>          I got the same density pattern by using our own code when
> taking the .gro file as the input trajectory.  The bin size is .052nm
> and the gro file is written with 3 decimal places, so there should be
> enough resolution in the output to avoid artifacts.
>          We are concerned about the integrity of the gro file produced
> by trjconv because we need to analyze our trajectories and don't know a
> better alternative than extracting coordinates with trjconv.
>          Below are the scripts I used to convert the .trr to .gro and
> extract the density:
>   trjconv -f ***.trr -s ***.tpr -o ***.gro
>   g_density -f ***.trr(***.gro) -s ***.tpr -o density.xvg -number -sl 250
>          The version of Gromacs is 3.3.3, with single precision.
>          Thanks for your help.

How large is the water box? What is the scale of the x-axis in your plots?


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