[gmx-users] Density Problem

Zhang Hui horsen at gmail.com
Mon Apr 27 01:51:06 CEST 2009

The water box is about 10nm in z direction. x and y box sizes are about


On Fri, Apr 24, 2009 at 7:17 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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?
> Mark
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