[gmx-users] Re: Isovalue for g_spatial representation

Eudes Fileti fileti at gmail.com
Sat Oct 30 13:11:29 CEST 2010

Dear Chris, thank you for information, they were very enlightening.
Just one more question. Suppose I use an isovalue, say 10, I can
say that the drawn surface is 10 times the average number density of solvent
molecules? I am using -div option.


Eudes Eterno Fileti
Física da Matéria Condensada
Simulação Computacional de Nano-estruturas via Dinâmica Molecular

> Message: 2
> Date: Fri, 29 Oct 2010 19:53:38 -0400
> From: chris.neale at utoronto.ca
> Subject: [gmx-users] Isovalue for g_spatial representation
> To: gmx-users at gromacs.org
> Message-ID: <20101029195338.kzvrdcvjr440ckk0 at webmail.utoronto.ca>
> Content-Type: text/plain;       charset=ISO-8859-1;     DelSp="Yes";
>        format="flowed"
> eef,
> I wrote g_spatial.
> If you use the -nodiv option, then the iso-value represents the number
> of counts in that bin over the entire trajectory divided by the number
> of frames. Therefore the units would be "atomic occupancy counts per
> frame". Note that, as for all such histograms, the values of isolines
> and isosurfaces are dependent on bin size.
> If you use the -div option (default), then the counts (already divided
> by the number of frames) are further divided by the number of atoms in
> the selection and then multiplied by the number of cells (similar to
> dividing by the volume of each cell). It's really a lot like an RDF: a
> number density per grid divided by the overall system density. It is,
> however, related to this by some multiplicative constant. You can find
> that because at the end of a g_density -div run, you will get an
> output of exactly what this divisor was, so you can go in using awk or
> whatever you like and modify the values as you see fit, turning values
> into proper densities if you like. Alternatively, you can run -nodiv
> and then divide all the the values yourself to get a proper density.
> Chris.
> -- original message --
> Hello gmx-users.
> I calculated the spatial distribution functions for my solvent-solute
> system.
> However I am in doubt in relation to the isovalue to be used in VMD to
> control
> the representation of the surface. The isovalue is admensional number or
> has
> some unit?
> There is some special criterium to choose its value?
> Thank you in advance.
> eef
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