[gmx-users] Ionic liquid simulation problem

Justin Lemkul jalemkul at vt.edu
Thu Sep 14 01:41:05 CEST 2017

On 9/13/17 5:55 PM, Agatha Faria 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 add the other specie (anion) 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. Tried to used the grompp command to minimize the energy of the 
> cations+anions box and got the following error:
> Fatal error:
> Too many warnings (18), gmx terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> 6. Using a -maxwarn option got the following error:
> Error in user input:
> Invalid command-line options
> In command-line option -maxwarn
> Too few (valid) values
> Does anyone knows whats is wrong with such a protocol?

The 18 warnings that were issued tell you what your problems are, but 
you haven't shared those.  Do not use -maxwarn.  A grompp warning 
indicates that something is badly wrong.  "Notes" are advice, and 
"warnings" are signals of danger.  Don't bypass the warnings.  Fix them.



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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