[gmx-users] problem with g_density

[vinothkumar mohanakrishnan]

Hi all

I also faced a similar problem like Ozge Engi when i used the g_density
command for water-DCE interface. when i saw the final .gro file in VMD i saw
some 20-25 molecules of water came on one side (end of DCE side) of the box
and  few molecules of DCE say 5 molecules on the end of water side. i have
attached the graph that i got. what is the problem due to? why are we not
getting the density profile starting from zero on both side of the box? any
help is highly appreciated.

Regards
Vinoth

On Mon, Oct 25, 2010 at 4:36 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi,
>
> > You're not
> > seeing complete mixing of your two species, but there is some diffusion
> > between the phases, otherwise both of your particles should drop to
> exactly
> > zero density on either side of the box middle, wouldn't they?
>
> No, not if there are undulations of the interface.
>
> Cheers,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101109/38442242/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: densityprofile
Type: application/octet-stream
Size: 13219 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101109/38442242/attachment.obj>