Quoting Manik Mayur <[email protected]>:
> > Exact command lines are much more useful than your interpretation of what > > you > > typed. If you just used genion -nn, that's probably insufficient > > information. > > > > Sorry for the confusion but genion won't add "Cl-" on its own unless I > provide it with the relevant options (providing which I thought would be > impertinent here). The only concern here was to find out "why Cl was listed > in the [ molecules ] section of the topol.top file", hence the error as no > such molecule was defined. > > But I found a workaround as to generate a .pdb file using genion, and then > use pdb2gmx to generate .gro and topol.top files, which I see automatically > generates a .itp file corresponding to "Cl-" and #includes it in topol.top > apart from adding it into [ molecules ] section. So now its working but the > question no. 3 is still on :) > I guess that works, but it's incredibly convoluted. If you provide genion a complete command line, then it should work fine, i.e.: genion -s input.tpr -p topol.top -nn 5 -nname CL- -random The above should be sufficient to insert 5 Cl- ions into your system, and update your topology accordingly. <snip> > Again sorry for the confusion(and I know its not magic :)) but "apart" from > providing the ion name to be added etc., according to the manual, you can > add ions by following ways- > 1) provide no. of ions to be added by -nn. > 2) use -neutral so that if the system already has a net charge, that will be > compensated. > 3) use -conc. To get (2) and (3) to work, simply specify -pname and -nname; if this is unclear in the manual perhaps some additional information would be useful, but truly you should probably always default to specifying these options yourself; the defaults are for ffgmx, which is deprecated. If you specify -pname and -nname, then genion will always work properly for the above command flags. <snip> > > > I can't comment on this specifically, but have you tried it? Does it give > > some > > sort of error message if you do? > > > I tried using above but grompp says its not possible. Meanwhile, I read in a > paper(JCP2003(118),4692-4701) that they used a modified PME with 3 times > bigger box dimension in the z-direction than the slab geometry. And I am > using it with periodicity=xyz turned on. > > So unless I use walls, I can't use periodicity=xy with coulumb-type=PME and > ewald_geom=3dc, Is that right? > Seems like that should be right; what is the exact error message that grompp is giving you? That is more informative than saying "its not possible." -Justin ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [email protected] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.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
