Re: [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.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Ionic liquid simulation problem

[Ednilsom Orestes]

Hi Ghosh,

Thanks for your answer.
But I'm not sure if I understood what you meant.
I already used insert-molecules command to create a box with the cationic
species.
Now, should I use the same command to include the anionic species into the
box?

Best



*Prof. Dr. Ednilsom OrestesDepartamento de Ciências Exatas - Sala C19Escola
de Engenharia Industrial Metalúrgica de Volta Redonda*

*Universidade Federal FluminenseR. dos Trabalhadores, 420 - Vila Santa
Cecília*
*Volta Redonda**, Rio de Janeiro, Brasil*
*CEP 27255-125*
*Tel: +55-24-2107-3777*


2017-09-05 17:24 GMT-03:00 soumadwip ghosh :

> Hi,
>
> I am not sure why you used the gmx solvate command for putting the
> anionic species in your simulation box. It is meant for filling up the
> simulation box with water molceules as the resname 'SOL' in the
> topol.top file. Thus when you hit grompp it expects 'SOL' entry in
> your topology file, cant find it and prints an error. In my opinion,
> one should use the same gmx insert-molecules command for inserting the
> anionic part into the box. If you dont want to use water in the
> simulation you can proceed without the solvation step but cant use gmx
> solvate for inserting anionic species or anything else.
>
> Best
> Soumadwip Ghosh
> Post Doctoral Research Associate
> City of Hope Cancer Research Center
> Duarte 91010 CA
> USA
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Re: [gmx-users] Ionic liquid simulation problem.

[Justin Lemkul]

On 9/5/17 2:32 PM, Ednilsom Orestes 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 used the *solva**te* command to add the other specie
(anion) as solvent 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. I them tried to used the *grompp* command to minimize the energy of the
cations+anions box and got the following error:

Fatal error:
Syntax error – File forcefield.itp, line 20
Last line read:
‘1 3yes   0.5  0.5'
Found a second defaut directive.

Does anyone knows whats is wrong with such a protocol?



This means you've got a syntactically invalid force field file, as you're trying 
to set two [defaults] directives (the actual instructions for the force field 
functional form, so there can only be one).


-Justin

--
==

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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Re: [gmx-users] Ionic liquid simulation problem

[soumadwip ghosh]

Hi,

I am not sure why you used the gmx solvate command for putting the
anionic species in your simulation box. It is meant for filling up the
simulation box with water molceules as the resname 'SOL' in the
topol.top file. Thus when you hit grompp it expects 'SOL' entry in
your topology file, cant find it and prints an error. In my opinion,
one should use the same gmx insert-molecules command for inserting the
anionic part into the box. If you dont want to use water in the
simulation you can proceed without the solvation step but cant use gmx
solvate for inserting anionic species or anything else.

Best
Soumadwip Ghosh
Post Doctoral Research Associate
City of Hope Cancer Research Center
Duarte 91010 CA
USA
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