Hi James, It's probably better to put all the molecules in the original box (trjconv -pbc mol), and then delete all molecules with an atom with z<0 or z>9.7. In addition, why not use a hexagonal prism to limit the size of your system further? Saves and additional 14%.
Hope it helps, Tsjerk On Fri, Dec 21, 2012 at 8:23 AM, James Starlight <[email protected]>wrote: > Dear Gromacs users! > > > I have a protein embedded in membrane surrounded with 2 uipper and > lower water leafleates. I decide to decrease number of water in that > system (in both leafletes) by reducing its size in Z-dimension. > Firstly I've defined new box vectors of my system via editconf and > than I've uded genbox to cut water in both upper and lower leaflets > genbox -cs b2ar_Smaller.gro -box 8.68740 8.41864 9.70145 > > here 9.70145 is the new size of the Z dim (vs 12.0 in old version. > > That produce system with desireble water\lipid ratio but atom order in > protein was perturbed. How I could fix such problem or reduce system > size by different methods ? > > > James > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
