[gmx-users] the details about g_density

vigaryang vigar_yang at hotmail.com
Thu May 23 15:32:49 CEST 2013

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? 

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:


The issue also has some useful information about how g_density works, which of 
course can also be obtained from the code itself.


> 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


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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