vinothkumar,
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.
Chris.
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.
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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