Hi, I have a system consists of a box of water and a monolayer of polymer in the center. I am trying to extract solvent molecules that have z coordinates greater than 5 nm using g_select and output an index file. Basically I want to separate my system into two portions: a box of waters above the monolayer and the rest of the system containing the monolayer. With the water only portion extracted by trajconv, I want to use genion to replace some water molecules with salt and put this modified portion back to my system that contains the monolayer.
Right now, I am able to use g_select -on -select "resname SOL and z>5" to select all atoms that belong to SOL and has z > 5 nm. However, this way does not guarantee that all the atoms selected are from SOL molecules whose cog are above z=5 plane. And as a result, some atoms that are part of SOL molecules below the z=5 plane are also selected and the entire selection contains some complete water molecules and some atoms that are from below plane water molecules (incomplete waters). I am not sure with this kind of selection, if I extract it with trajconv, and replace water with salt by genion, and then put it back to original system, will I get correct alignment of those atoms from incomplete water molecules and get the desired configuration. ( I think genion will only replace complete residue; however, when using trajconv to generate new coordination files, I am not sure if the system will be re-set to origin or not. If so then the coordinates will definitely be misplaced and when I put the modified part back there will be misalignment). TO AVOID all that, I'd like to use "cog of SELECTION" option in the g_select, except for 1 problems: the -on option only works with atom selection. So my essential question is: is there a way to use g_select with both the -on option and cog option? Or is there another way to finish my task? I have searched the archive and did not find something that answers my question. Thank you all for helping out. Best, Dongxu Huang Graduate student at Northwestern University -- 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.
