Quoting Manik Mayur <manik.ma...@gmail.com>: > On Sat, Dec 27, 2008 at 3:12 PM, Manik Mayur <manik.ma...@gmail.com> wrote: > > > Hi all, > > > > I have a few probIems/confusions and will be extremely thankful for any > > help. I added some "Cl- ions" by replacing water using "genion (and -nn)". > > It generated a "topol.top" file with Cl listed in [ molecules ]. Now when I > > try to run grompp, it gives an error saying "no such molecule type Cl". So > > my questions are:
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. > > 1) How to avoid that error? Do I have to define a Cl.itp and add molecule > > type etc. ? Check ions.itp for the proper ion nomenclature for whatever force field you're using. Different force fields use different naming. > > 2) If I try to add Cl using -neutral option (as my system before already > > had a net +ve charge), it says "No ions to add and no potentials to > > calculate", why? Probably because your command line was just genion -neutral, right? You didn't tell genion what type of ions to add, so it's not going to do anything; it's not magic! > > 3) Why is Cl listed in molecules and not [atoms] section? If you properly #include "ions.itp" then it is an additional moleculetype definition within the topology. > > 4) If I wish to use SPC/E model, do I have to use ffgmx*. I tried using > > ffG43a1* with #include "spce.itp" in topol.top. Is that correct? what else > I You should not use ffgmx for anything. Using #include "spce.itp" is correct for use with other force fields. > > would have to do? > > 5) Is it mandatory to have periodicity=xyz with coulumb-type=PME and ewald > > geom=3dc, other than using walls option(I have my own channel walls in the > > system, so want to avoid them). Is there a way to use periodicity=xyz with > > coulumb-type=PME and ewald geom=3dc? > > > Is there a way to use periodicity=xy with coulumb-type=PME and ewald > geom=3dc? > > I can't comment on this specifically, but have you tried it? Does it give some sort of error message if you do? -Justin > > Thanks, > > Manik > > > > -- > > _________________ > > HAPAX LEGOMENA > > > > > > -- > _________________ > HAPAX LEGOMENA > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
