Dear Gromacs users, I am writing to ask about g_densmap command:
If there are species adsorbed (stagnant) or structured around a frozen group, for which I want to obtain the density distribution map, g_densmap calculates unrealistically high densities. (like 2000 /nm3 of water...). So in visualization, the regions with descent density (like ~ 30 /nm3 for bulk water) will be shown with the same color code as zero density (because .xpm supports only 16 colors). I was wondering if there was a way to obtain the numerical density values (in a 2d matrix) as the output of g_densmap, rather than the .xpm format. (One solution is to impose the maximum with an educated guess for -dmax option, but having the actual numbers would be nicer.) Furthermore, I was wondering if there is readily a code available to convert the .xpm image to a matrix with numerical values, if I want to do a calculation on the density map. Currently I convert the .xpm file to .png, then import it to MATLAB and use the image processing toolbox to analyze. I believe this introduces some error to the calculation. I look forward to receiving your advice! Thank you, Amin -- Amin Nouri MSc student Chemistry department, Simon Fraser University -- View this message in context: http://gromacs.5086.n6.nabble.com/g-densmap-adsorbed-species-and-output-format-tp5003678.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
