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

Justin A. Lemkul jalemkul at vt.edu
Sun Dec 28 00:17:28 CET 2008

Quoting Manik Mayur <manik.mayur at gmail.com>:

> > 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.


> 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.


> > 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 A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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