[gmx-users] problem with g_density

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 9 12:59:31 CET 2010

vinothkumar mohanakrishnan wrote:
> 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.

The thread you quote contains the answer.  The densities likely will not go 
completely to zero; the layers interact with each other in some way, so there 
will be some fluctuations at the interface between the two.


> Regards
> Vinoth
> On Mon, Oct 25, 2010 at 4:36 PM, Tsjerk Wassenaar <tsjerkw at gmail.com 
> <mailto: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
>     --
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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