[gmx-users] problem with g_density

[Justin A. Lemkul]

chris.neale at utoronto.ca wrote:
> 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.
> 

As of version 4.5.2, this should be fixed.  Berk implemented per-frame 
normalization on Sept. 14.

-Justin

> 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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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