[gmx-users] problem with g_density

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Nov 9 14:48:30 CET 2010


The roughness of the interface that Justin is suggesting is only one  
possible explanation for this feature. The other possible explanation  
is that you are running a NPT simulation and your volume fluctuations  
are causing the Z-dimension to fluctuate. In this case, g_density will  
give somewhat incorrect results exactly like this. While I suspect  
that there is at least some interface spatial roughness that is  
contributing to your result, there is no way to tell from your plot if  
this is the dominant reason for apparent mixing, or if, rather, the  
mixing is mostly temporal based on z-axis fluctuations and not much  
spatial mixing at all.

There are probably trjconv-based solutions to your problem, but at a  
first pass I'd say that g_density is broken so don;t use it.


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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