The water box is about 10nm in z direction. x and y box sizes are about 3.3nm.<br><br>Hui<br><br><div class="gmail_quote">On Fri, Apr 24, 2009 at 7:17 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">Zhang Hui wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear All,<br>
<br>
I just found that there is a problem when I extract the density<br>
of water from my Gromacs simulations.<br>
<br>
When I used g_density to get the water density from .trr<br>
trajectory file, the density plot looked normal. But when I used trjconv<br>
to convert the .trr to .gro file, and then used g_density to get the<br>
water density from .gro trajectory file, there was an unusual<br>
periodicity in the densities. The density comparison plot is attached.<br>
<br>
I got the same density pattern by using our own code when<br>
taking the .gro file as the input trajectory. The bin size is .052nm<br>
and the gro file is written with 3 decimal places, so there should be<br>
enough resolution in the output to avoid artifacts.<br>
<br>
We are concerned about the integrity of the gro file produced<br>
by trjconv because we need to analyze our trajectories and don't know a<br>
better alternative than extracting coordinates with trjconv.<br>
<br>
Below are the scripts I used to convert the .trr to .gro and<br>
extract the density:<br>
<br>
trjconv -f ***.trr -s ***.tpr -o ***.gro<br>
g_density -f ***.trr(***.gro) -s ***.tpr -o density.xvg -number -sl 250<br>
<br>
The version of Gromacs is 3.3.3, with single precision.<br>
Thanks for your help.<br>
</blockquote>
<br></div></div>
How large is the water box? What is the scale of the x-axis in your plots?<br>
<br>
Mark<br>
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</blockquote></div><br>