[gmx-users] problem with g_density
Justin A. Lemkul
jalemkul at vt.edu
Tue Nov 9 14:53:14 CET 2010
chris.neale at utoronto.ca wrote:
> 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.
As of version 4.5.2, this should be fixed. Berk implemented per-frame
normalization on Sept. 14.
> 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
> 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
> 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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