[gmx-users] Density Problem

Zhang Hui horsen at gmail.com
Fri Apr 24 20:30:00 CEST 2009

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.

Hui Zhang
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