[gmx-users] Ionic liquid simulation problem

[Justin Lemkul]

I answered this the other day:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-September/115865.html

-Justin

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

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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