[gmx-users] Ionic liquid simulation problem

[Justin Lemkul]

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

-- 
==================================================

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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================