[gmx-users] Re: genion and a few other problems

[Manik Mayur]

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>
> 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
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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-- 
_________________
HAPAX LEGOMENA
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