[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.
> On Mon, Oct 25, 2010 at 4:36 PM, Tsjerk Wassenaar <tsjerkw at gmail.com
> <mailto:tsjerkw at gmail.com>> wrote:
> > You're not
> > seeing complete mixing of your two species, but there is some
> > 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.
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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