Hello Dear User, I am confused about the normalization in the g_rdf command. It should be noted that I understand the meaning of RDF but am not sure about the definition of RDF in GROMACS in detail.
When I calculate the rdf of Hydrogen (HW) of water molecules around one Oxygen (OW) of one water molecule, I do not want the normalized option, and thus I use the -nonorm in g_rdf, which indicate that no Normalization is conducted for volume and density. I checked the results, namely the HW number distribution at different radical distances (R), the minimum value is 500, which is quite impossible. What the meaning of these value? Are these value means the HW numbers at different radical distance ? Additionally, all HW numbers are integral times of 500. In order to confirm this result, I normalize the data myself: dividing these values by the volume of the shell layer (4*pi*R^2*dl) and the average water density (33.4 N/nm^3). However, these calculated results is several order higher than the normalized results by Gromacs with default -norm option. Thanks in advance. Haiyang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.