Re: [gmx-users] the details about g_density
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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Re: [gmx-users] the details about g_density
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: 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] the details about g_density
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? 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
