Hi Everyone, I am having an awkward situation. I want to use g_density to get the density profile of a lipid bilayer. At first glance, it looks like a trivial task. But for my case, it's not because I have conflicting atom names from two different molecules. I am using GROMOS 53a6. In DPPC topology, I have C1 C2 C3 N4...O7... In another lipid topology, say lipid B, I have C1 C2 C3 N4... C7...
The C1 in DPPC and C1 in lipid B could have different atomic mass as GROMOS is united atom representation. C1 of DPPC could be a CH2, C2 of lipid B could be a CH3. Then I don't know how to specify the entry in the .dat file: C1 = ? Is it possible to calculate the density profile of the whole bilayer by just invoking g_density once? Or in my awkward situation, I have to calculate the density profile of each molecule type, then add them together? Then I will be concerned with the numerical errors involved. Thanks. Bin -- 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
