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.
Bests eef _______________________________________ 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.ne...@utoronto.ca > Subject: [gmx-users] Isovalue for g_spatial representation > To: gmx-users@gromacs.org > Message-ID: <20101029195338.kzvrdcvjr440c...@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 > > > > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 78, Issue 225 > ****************************************** >
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