The water box is about 10nm in z direction. x and y box sizes are about 3.3nm.
Hui On Fri, Apr 24, 2009 at 7:17 PM, Mark Abraham <mark.abra...@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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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