[gmx-users] g_density for a centain slice

li jianguo ljgsq at yahoo.com
Wed Feb 25 08:10:52 CET 2009

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,
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.


    From: "Berk Hess" <[EMAIL PROTECTED]>
    Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
    To: gmx-users at 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 at gromacs.org>
        To: gmx-users at 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

    Not without editing the code.
    But it should not be do difficult to edit the code to make
    g_densmap do what you want.


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.


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