[gmx-users] Re: genion and a few other problems
manik.mayur at gmail.com
Sat Dec 27 15:56:55 CET 2008
On Sat, Dec 27, 2008 at 6:36 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Quoting Manik Mayur <manik.mayur at gmail.com>:
> > On Sat, Dec 27, 2008 at 3:12 PM, Manik Mayur <manik.mayur at gmail.com>
> > > 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
> > > 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".
> > > my questions are:
> Exact command lines are much more useful than your interpretation of what
> typed. If you just used genion -nn, that's probably insufficient
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
> > > type etc. ?
> Check ions.itp for the proper ion nomenclature for whatever force field
> using. Different force fields use different naming.
> > > 2) If I try to add Cl using -neutral option (as my system before
> > > 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
> tell genion what type of ions to add, so it's not going to do anything;
> 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
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
> > 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
> > > geom=3dc, other than using walls option(I have my own channel walls in
> > > system, so want to avoid them). Is there a way to use periodicity=xyz
> > > 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
> 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?
> > Thanks,
> > > Manik
> > >
> > > --
> > > _________________
> > > HAPAX LEGOMENA
> > >
> > --
> > _________________
> > HAPAX LEGOMENA
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
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