Hi all<br><br>I also faced a similar problem like<span style="color: rgb(51, 0, 0);"> </span><span style="color: rgb(51, 0, 0);" class="gI"><span class="gD">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.<br>
<br>Regards<br>Vinoth<br></span></span><br><div class="gmail_quote">On Mon, Oct 25, 2010 at 4:36 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi,<br>
<div class="im"><br>
> You're not<br>
> seeing complete mixing of your two species, but there is some diffusion<br>
> between the phases, otherwise both of your particles should drop to exactly<br>
> zero density on either side of the box middle, wouldn't they?<br>
<br>
</div>No, not if there are undulations of the interface.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
<div><div></div><div class="h5">--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br>