[gmx-users] Ionic liquid simulation problem

Justin Lemkul jalemkul at vt.edu
Fri Sep 15 13:59:01 CEST 2017

I answered this the other day:



On 9/14/17 9:55 AM, 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?
>> Thanks in advance.
>> Ágatha


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

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