[gmx-users] genion and a few other problems

Manik Mayur manik.mayur at gmail.com
Sat Dec 27 10:42:16 CET 2008

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",
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?


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