[gmx-users] Ionic liquid simulation problem.

Ednilsom Orestes eorestes at gmail.com
Tue Sep 5 20:33:29 CEST 2017

Dear GROMACS Community,

I am very new with GROMACS I am trying to run a simulation of an ionic
liquid (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to
the following protocol:

1. Prepared the respective PDB files and added/modified the OPLS/AA force
field parameters updating the atomtypes.atp, aminoacid.rtp, ffbonded.itp
and ffnonbonded.itp files.

2. Used *pdb2gmx* command to create the respective .gro files, as well as,
the posre.itp and topol.top files chossing OPLS/AA option without solvation.

3. Used the *insert-molecules* command to create a box filled with one
specie (cation) and used the *solva**te* command to add the other specie
(anion) as solvent into the same box.

4. Updated, by hand, the generated topol_box.top (pos_box.top) file
including the topol.top and the posre.itp files of the other specie (anion)
at the end of it.

5. I them tried to used the *grompp* command to minimize the energy of the
cations+anions box and got the following error:

Fatal error:
Syntax error – File forcefield.itp, line 20
Last line read:
‘1                 3            yes           0.5      0.5'
Found a second defaut directive.

Does anyone knows whats is wrong with such a protocol?

Thanks in advance.


*Prof. Dr. Ednilsom OrestesDepartamento de Ciências Exatas - Sala C19Escola
de Engenharia Industrial Metalúrgica de Volta Redonda*

*Universidade Federal FluminenseR. dos Trabalhadores, 420 - Vila Santa
*Volta Redonda**, Rio de Janeiro, Brasil*
*CEP 27255-125*
*Tel: +55-24-2107-3777*

More information about the gromacs.org_gmx-users mailing list