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 <tsje...@gmail.com
<mailto:tsje...@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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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