Hi On Thu, Jan 27, 2011 at 16:18, Manuel Nuno Melo <m.n.m...@rug.nl> wrote: > My idea is to count the number of water molecules within a certain z > distance of the bilayer center, and flag a pore above a certain threshold. > The problem is that the position of this z-slab cannot be hardcoded because > my simulations are relatively long and there is sometimes a drift of the > bilayer. > > also fails because the pore is lined by peptide molecules and a relatively > large distance for the PW-C4 distance must be allowed. This means that > interfacial waters will be frequently counted in.
This is unfortunately not possible with the current version of g_select, as the number of available keywords is quite limited. If you want to do some programming, it should be relatively straightforward (although the learning curve for the selection engine can be quite steep) to add new keywords. There is some documentation in the headers selmethod.h and selparam.h, and you should be able to implement, e.g., a selection keyword like "zwithin 0.5 of com of name ..." by looking at the existing implementations in sm_distance.c (contains, e.g., 'within' and 'dist') and sm_simple.c (contains, e.g., 'z'). Best regards, Teemu -- 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
