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
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[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
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From: "Berk Hess" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: [email protected]
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 <[email protected]>
To: [email protected]
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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