[gmx-users] Ionic liquid simulation problem

Agatha Faria agathafaria at icloud.com
Wed Sep 13 23:56:01 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 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?

Thanks in advance.


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