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

Manik Mayur manik.mayur at gmail.com
Sat Dec 27 10:44:21 CET 2008

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:
> 1) How to avoid that error? Do I have to define a Cl.itp and add molecule
> type etc. ?
> 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?
> 3) Why is Cl listed in molecules and not [atoms] section?
> 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
> 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
> Thanks,
> Manik
> --
> _________________

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