On Sat, Dec 27, 2008 at 6:36 PM, Justin A. Lemkul <[email protected]> wrote:
> Quoting Manik Mayur <[email protected]>: > > > On Sat, Dec 27, 2008 at 3:12 PM, Manik Mayur <[email protected]> > 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. > 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 :) > > 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. ok > > > > > 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! > 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. The first one works, but the second one is giving the above mentioned error. > > 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. > ok > > 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? 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? -Justin > Thanks, Manik > > Thanks, > > > Manik > > > > > > -- > > > _________________ > > > HAPAX LEGOMENA > > > > > > > > > > > -- > > _________________ > > HAPAX LEGOMENA > > > > > > ======================================== > > 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 > -- _________________ HAPAX LEGOMENA
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