[gmx-users] the details about g_density

[Justin Lemkul]

On 5/23/13 9:32 AM, vigaryang wrote:
> Thanks very much for your reply.Fortunately,I have used g_density in NVT systems.  Does the expression " it is built from the coordinate origin outward" mean that the mass density profile is calculated based on the average of the coordination and weight of each atom of the molecule?
>

You asked if density profiles were built from the center of mass, which they are 
not.  Masses/charges are binned across the desired box vector like histograms, 
with the number of slices (and thus implicitly the bin width determined by the 
-sl option), and bins are constructed from the zero point of the axis upward.

-Justin

>
> With best wishes,
>
> Qiwei Yang
>
>
> ----- Original Message -----
> From: Justin Lemkul
> To: Discussion list for GROMACS users
> Date: 2013-05-23, 19:54:11
> Subject: Re: [gmx-users] the details about g_density
>
>
> On 5/22/13 9:12 PM, vigaryang wrote:
>> I have used the program "g_density" to generate the mass density profile and the charge density profile of molecules at gas-liquid interface. My question is: Is the center of mass/charge used by g_density to compute the the mass/charge density profile?
>>
>
> No, it is built from the coordinate origin outward. Note that there are
> problems with g_density when using NPT and/or complex systems:
>
> http://redmine.gromacs.org/issues/1168
>
> The issue also has some useful information about how g_density works, which of
> course can also be obtained from the code itself.
>
> -Justin
>
>> I'm eager for the answer, because the reviewer of my submitted article ask me for that question but I don't know how to reply. I have used google to search for the answer, but I did not found.
>>
>> I really appreciate you for the attention and consideration to this email.
>>
>>
>> Best regards,
>>
>> Vigar Yang
>>
>> Department of Chemical and Biological Engineering,
>> Zhejiang University,
>> Hangzhou, China
>>
>>
>>
>>
>
>
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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