<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">Dear Chris, thank you for information, they were very enlightening.<div>Just one more question. Suppose I use an isovalue, say 10, I can </div><div>say that the drawn surface is 10 times the average number density of solvent<br>
molecules? I am using -div option.</div><div><br></div><div>Bests</div><div>eef<br><div><br></div><div>_______________________________________<br>Eudes Eterno Fileti<div>Física da Matéria Condensada</div><div>Simulação Computacional de Nano-estruturas via Dinâmica Molecular</div>
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Message: 2<br>
Date: Fri, 29 Oct 2010 19:53:38 -0400<br>
From: <a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a><br>
Subject: [gmx-users] Isovalue for g_spatial representation<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:20101029195338.kzvrdcvjr440ckk0@webmail.utoronto.ca">20101029195338.kzvrdcvjr440ckk0@webmail.utoronto.ca</a>><br>
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<br>
eef,<br>
<br>
I wrote g_spatial.<br>
<br>
If you use the -nodiv option, then the iso-value represents the number<br>
of counts in that bin over the entire trajectory divided by the number<br>
of frames. Therefore the units would be "atomic occupancy counts per<br>
frame". Note that, as for all such histograms, the values of isolines<br>
and isosurfaces are dependent on bin size.<br>
<br>
If you use the -div option (default), then the counts (already divided<br>
by the number of frames) are further divided by the number of atoms in<br>
the selection and then multiplied by the number of cells (similar to<br>
dividing by the volume of each cell). It's really a lot like an RDF: a<br>
number density per grid divided by the overall system density. It is,<br>
however, related to this by some multiplicative constant. You can find<br>
that because at the end of a g_density -div run, you will get an<br>
output of exactly what this divisor was, so you can go in using awk or<br>
whatever you like and modify the values as you see fit, turning values<br>
into proper densities if you like. Alternatively, you can run -nodiv<br>
and then divide all the the values yourself to get a proper density.<br>
<br>
Chris.<br>
<br>
-- original message --<br>
<br>
Hello gmx-users.<br>
I calculated the spatial distribution functions for my solvent-solute<br>
system.<br>
However I am in doubt in relation to the isovalue to be used in VMD to<br>
control<br>
the representation of the surface. The isovalue is admensional number or has<br>
some unit?<br>
There is some special criterium to choose its value?<br>
Thank you in advance.<br>
eef<br>
<br>
<br>
<br>
<br>
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End of gmx-users Digest, Vol 78, Issue 225<br>
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