On 10/7/12 12:13 PM, Andrew DeYoung wrote:
Hi,
My system is in the slab geometry; I have applied periodic boundary
conditions along x and y, but none along z.
I frequently use the handy tool g_potential (using the -oc switch) to
compute the (average) charge density (i.e., charge distribution or a
"histogram of charges") along z for a particular group specified by an index
file entry. Since the partial charges are discretely assigned to individual
atoms, this means that the -oc switch of g_potential effectively gives me a
sort of distribution of the atoms along z, although the units are charge
density, of course.
My question is, what if I have atoms with zero partial charge? Of course,
such atoms do not contribute to the charge density. But what if I would
still like to compute some sort of distribution of these atoms along z?
One idea is to use g_traj to print all of the z-coordinates of a particular
group over time to an .xvg file. Then, using a scripting language, I could
"bin" the z-coordinates and then average over time. But is there already a
Gromacs utility that does this?
It seems that g_density, with the "-dens number" switch, may accomplish
this. Is it true that the "-dens number" switch will lead to computation of
the number density of _each_ atom which is specified in the index file
entry?
Seems about as good of an approach as any. You can certainly come up with a
test case and use g_density to see if it meets expectations.
-Justin
--
========================================
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 [email protected]
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 [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
