Dear all, I have a surface in xy plane. I want to use g_density to calcuate the density profile of solvent along z axis. As my surface groups is not homogeneuously distributed on the surface, some parts are hydrophilic and some parts are hydrophobic. therefore I need to divide the surface into several slice. Is it possible to use g_density for one slice? I searched the previous posts, and found several others met the same difficulty. From previous posts by Berk, it seems this function has been imcoporated into gromacs, but I did not find in the manual. Btw, I am using Gromacs 3.3.3. Anyone have solutions? Thanks very much, Jianguo Dept. Chemcial and Biomolecular Engineering National University of Singapore -------------------------------------------------------------------------------------------------------------------------
[gmx-users] g_densmap per slice Sung Hyun Park Fri, 25 Jan 2008 13:55:01 -0800 I need to calculate the density maps (or preferably density data) on xy-plane for each "slice" along z, but g_densmap and g_density seem to calculate only the" average" density over z direction. I searched and found the following discussion about a similar topic last September. According to Berk in the discussion, g_densmap in gromacs-3.3.2 should now be able to calculate the density map per slice. Does anyone know if that is indded so and, if so, how do I use that option? I searched the manual on g_densmap in gromacs-3.3.2 but couldn't find the option. BTW my gromacs version is 3.3.1, I assume I cannot use that new option. Is there any simple way to do the job on the old version 3.3.1? I am a gromacs beginner and have little programming skill. Any help and/or advice would be greatly appreciated. Sung --------------------------------------------------------------------------------------------------------------------------- From: "Berk Hess" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org> To: gmx-users@gromacs.org Subject: RE: [gmx-users] g_densmap per slice Date: Fri, 21 Sep 2007 11:16:21 +0200 From: gil claudio <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org> To: gmx-users@gromacs.org Subject: [gmx-users] g_densmap per slice Date: Fri, 21 Sep 2007 01:37:45 -0700 (PDT) Is there a way to use g_densmap for a slice of the box? For example, g_densmap can average the density of a box on the x-y plane, and thus average through the z-axis. If, for example, the z-axis is 10 nm deep, can I use g_densmap to get a slice along the z-axis, for example, along the slice between 1nm to 2nm? Not without editing the code. But it should not be do difficult to edit the code to make g_densmap do what you want. Berk. This seems a useful option, so I have implemented it in CVS, also for the 3.3.2 release, which should hopefully come out today. Berk.
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