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

Justin A. Lemkul jalemkul at vt.edu
Sat Dec 27 14:06:56 CET 2008

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.

> > 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?


> > Thanks,
> > Manik
> >
> > --
> > _________________
> >
> --
> _________________


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


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