Potential for graphene oxide in water

As a first approach I have used opls-aa force field for studyng the behavior of carbon nanotube cluster in water with good results. I just found that opls-aa force field has been used previously for the case of graphene oxide in water (Langmuir, 2012, 28, pp 235–241). For opls-aa details and parameters, consider Jorgensen's publication and its supporting info file (J. Am. Chem. Soc., 1996, 118, pp 11225–11236 ).

best,

Eric Romero

Hi Eric,

Thank you so much for your reply.

I read these two papers before. I think opls-aa force field is a good choice for my simulations.

However, I am really confused with the atom types in opls-aa. There are too many atom types for carbon, hydrogen and oxygen atoms. I don’t know which I should choose for the functionalized and unfunctionalized carbon atoms, hydrogen and oxygen atoms in hydroxy and epoxy groups.

I downloaded the opls-aa force field parameter files from GROMACS, as in the attachment. And I also found the parameters on the website:
http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
http://lists.gromacs.org/pipermail/gmx-users/2012-January/067596.html

The numbers (opls_***) of atom types are totally different. I am so confused that I don’t which atom types to choose.

Can I use “CA : Aromatic C” for unfunctionalized carbon atoms in pristine graphene, “CA : Phenol C-OH” for functionalized carbon atoms, “OH : Phenol -OH” for oxygen atoms in hydroxy groups, and “HO : Phenol -OH” for hydrogen atoms in hydroxy groups? There are many atom types using the same capital abbreviation in the force field files. I don’t know which one to choose.

Can you give me some suggestions? I will appreciate that very much.

Thank you again.

Best,
Jason Zhu

2012/10/13 Eric Romero Blanco <eromerob@…3758…>

ffbonded.itp (216 KB)

ffnonbonded.itp (61.8 KB)

Hi Eric,

Thank you so much for your reply.

I read these two papers before. I think opls-aa force field is a good choice
for my simulations.

However, I am really confused with the atom types in opls-aa. There are too
many atom types for carbon, hydrogen and oxygen atoms. I don't know which I
should choose for the functionalized and unfunctionalized carbon atoms,
hydrogen and oxygen atoms in hydroxy and epoxy groups.

I downloaded the opls-aa force field parameter files from GROMACS, as in the
attachment. And I also found the parameters on the website:

you should read the OPLS-AA paper instead. please note that
gromacs uses a unit setting not supported by LAMMPS, so you
would have convert them. better to use the original. you get the
explanation of how to use the force field as a bonus.

axel.

Jason,
In the attachment you can find an example of how to read opls-aa force field parameters from http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm, those wich could be considered in an initial approach for working with non-reactive surfaces of graphene oxide. I think, you would find in the literature better opls-aa force field parameters, optimized for the application type you need.

best,

Eric Romero

example opls-aa.pdf (6.41 KB)

Hi Axel,

Thank you very much for your reply.

I have found some OPLS-AA papers for graphene oxide simulations. They may use some existing MD softwares and potential library files. In the method part of their papers, they only cite GROMACS or other MD packages and Jorgensen’s original paper (1996-OPLS). They seem to be avoiding to mention the specific atom types and potential parameters they use. It is hard for me to repeat their simulations.

At the time of Jorgensen’s original paper (1996), graphene still remains undiscovered. There is no specific atom types for carbon atoms in graphene. My major is not chemistry. I am not sure if I can use “CA : Aromatic C” for unfunctionalized carbon atoms in pristine graphene, “CA : Phenol C-OH” for functionalized carbon atoms.

I ever used the GROMACS. I know its unit system (length: nm; Energy: kJ/mol) is different from LAMMPS. Also, there is a 0.5 factor in some harmonic bond and angle formulas, which is not same as the OPLS original form.

I am still searching the OPLS papers for graphene oxide now. If you can provide some related papers or give me a suggestion for atom types, I will very appreciate that.

Thank you again.

Best,
-Jason

2012/10/14 Axel Kohlmeyer <[email protected]>

Hi Eric,

Thank you very much for your reply and the attached file.

It is very useful for me to understand how to use the OPLS force field parameters.

I still have some small questions. My major is not chemistry. I am not sure that if the chemical groups (hydroxyl) bonded, will the carbon atom in graphene change its hybridization?

In your example file, can I use parameters in “C(sp2): Aromatic C” for unfunctionalized carbon atoms in pristine graphene, parameters in “C (sp2) - OH” for functionalized carbon atoms and hydrogen-oxygen atoms (hydroxyl groups)?

Thank you again.

Best,
-Jason

2012/10/14 Eric Romero Blanco <eromerob@…3758…>

Hi Eric,

Thank you very much for your reply and the attached file.

It is very useful for me to understand how to use the OPLS force field
parameters.

I still have some small questions. My major is not chemistry. I am not sure

sorry, no empathy here. if you want to do something
*requires* chemical understanding then you have to
learn it. it is not too difficult to catch up on what you
need to know, but it is much better to find somebody
local. a mailing list is no replacement for learning the
fundamentals. *everybody* has to do through this.
you can't expect to drive a car, if you can't read the
traffic signs, don't have proper schooling and don't
have a driver's license either, or do you? you may
be able to drive around for a bit, but sooner or later
a big catastrophe will be looming around the corner.

axel.