[gmx-users] Ionic liquid simulation problem.

Justin Lemkul jalemkul at vt.edu
Wed Sep 6 00:31:25 CEST 2017

On 9/5/17 2:32 PM, Ednilsom Orestes wrote:
> 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?

This means you've got a syntactically invalid force field file, as you're trying 
to set two [defaults] directives (the actual instructions for the force field 
functional form, so there can only be one).



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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