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
--
========================================
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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