[gmx-users] using OH ions in combination with CHARMM27 force field

soumadwip ghosh soumadwipghosh at gmail.com
Thu Dec 10 14:57:58 CET 2015

Hi all,
         I am trying to simulate a polymer membrane in the presence of
electrolytes. As an effort to corroborate experimental outcomes I have to
do simulation in the presence of 0.1M NaOH. I know that OH- is present in
the standard CHARMM FF directory. So, I tried to add 15 Na (+) and 15 OH(-)
in the system which happened without any error. Now, while executing grompp
for energy minimization I got this strange error of the no. of coordinates
in the gro file does not match that of the .top file and the difference is
15 less in the .gro file. Now the thing is I can see that genion has added
the required no. of OH(-) in the system and the topology file has been
updated accordingly. However, if I add CL instead of the hydoxide ion
things go smoothly and grompp does not scream. Is there something anyone
knows about this kind of weird behavior of the ions? I am using GROMACS
5.0.5. Any sort of help will be appreciated. Following are my files-


; Include the force field
#include "charmm27.ff/forcefield.itp"

;Include CHARMM atomtypes
#include "atomtypes_nafion.itp"

; Include chain topologies
#include "nafion.itp"

; Include water topology
#include "charmm27.ff/tip3p.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; Include generic ion topology
#include "charmm27.ff/ions.itp"

[ system ]
nafion and ions in water

[ molecules ]
LIG             1
SOL            7997
NA              15
OH              15

Soumadwip Ghosh
Research Scholar

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