Justin, I tried to use an index file with atom numbers of the water molecules in the required volume.
But when I try to ionize the box, I get this error: Fatal error: The solvent group SOL is not continuous: index[717]=21689, index[718]=21696 This makes sense, but is there a way get around this? SR On Thu, Mar 25, 2010 at 5:17 PM, Justin A. Lemkul <[email protected]> wrote: > > > Smiruthi Ramasubramanian wrote: > >> >> I am simulating an ion channel and require help placing a concentration of >> ions at one side of the box (below the membrane). >> >> > "Sidedness" is irrelevant in a periodic system; the water layers are > continuous with PBC. > > > SETUP: membrane + embedded protein in the center of the cube. >> >> I tried to generate a smaller cube (of the required volume below the >> cube), solvate, add ions and then /cat/ with the *.gro file of my system >> before solvating. But when I solvate the system with ions, the ions are >> removed. >> >> Any suggestions as to how to handle this problem? >> >> > I don't fully understand what you tried to do, but it should be possible to > solvate the unit cell normally, create an index group for the waters on one > "side" of the membrane, and pass this index file to the -n flag of genion. > Creating the index file may involve writing your own script to collect the > atom numbers. As far as I am aware, make_ndx cannot, for example, select > all water molecules below/above some z-coordinate, which would be required > for your situation. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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