Graphene Oxide with AIREBO & CHARMM

​Hi Dears

I want to simulate Graphene Oxide with AIREBO and CHARMM force fields. I decided to use AIREBO for carbons of Graphene and CHARMM parameters for epoxy and hydroxyl groups . But i don’t know how to define parameters for them?

Thank you in advance

Regards

ISAAC

Hi Dears

I want to simulate Graphene Oxide with AIREBO and CHARMM force fields. I decided to use AIREBO for carbons of Graphene and CHARMM parameters for epoxy and hydroxyl groups . But i don't know how to define parameters for them?

mixing and matching force fields like this is a very, *very*, **VERY**
bad idea. those two are conceptually very different force fields, and
thus their parameterizations are not compatible. technically, it would
be possible to set up a simulation, but it would likely be more
flawed, that just using CHARMM for the whole system.

how to assign CHARMM atom types and/or parameterize those and create a
suitable topology file that can be correctly converted for use with
LAMMPS, is not a topic for this mailing list. you can ask about this
in the CHARMM forums.

axel.

Hi
There is an airebo FF for CHO on the S Sinnot web page.
Regards
Pascal

Hi Dears

I want to simulate Graphene Oxide with AIREBO and CHARMM force fields. I decided to use AIREBO for carbons of Graphene and CHARMM parameters for epoxy and hydroxyl groups . But i don't know how to define parameters for them?

mixing and matching force fields like this is a very, *very*, **VERY**
bad idea. those two are conceptually very different force fields, and
thus their parameterizations are not compatible. technically, it would
be possible to set up a simulation, but it would likely be more
flawed, that just using CHARMM for the whole system.

how to assign CHARMM atom types and/or parameterize those and create a
suitable topology file that can be correctly converted for use with
LAMMPS, is not a topic for this mailing list. you can ask about this
in the CHARMM forums.

axel.

Hi
There is an airebo FF for CHO on the S Sinnot web page.

i don't think it can work correctly with the AIREBO implementation in
LAMMPS. there are several places, where the code assumes, that there
are only two atom types in the parameter file and that one of them is
a hydrogen and the other a carbon.

axel.

Ok this is a very important information.
Else may be reaxFF can work ? I am not sure but I think I have seen some attempts.
A good way is to use google scholar with « graphene oxide reaxff » and look at what is proposed.

Regards
Pascal

Hi
There is an airebo FF for CHO on the S Sinnot web page.

i don't think it can work correctly with the AIREBO implementation in
LAMMPS. there are several places, where the code assumes, that there
are only two atom types in the parameter file and that one of them is
a hydrogen and the other a carbon.

axel.

Ok this is a very important information.
Else may be reaxFF can work ? I am not sure but I think I have seen some attempts.
A good way is to use google scholar with « graphene oxide reaxff » and look at what is proposed.

but look at the background of the people that do the simulations and
the focus of the journal the publication is in. these days, you can
get things published in journals, that don't have simulation/force
field experts as reviewers and thus don't look very carefully at the
specifics of the model (or don't have the skills to tell the
difference between a good and a not so good model).

what is a good choice strongly depends on the properties that one is
interested in. CHARMM or similar "generic" force fields can quite
suitable for some kinds of studies.
ReaxFF offers a much more flexible force field model, but then one has
to be more careful about transferability and the right
parameterization can give a much more accurate results (at
correspondingly higher computational cost). but in both cases, you
would stick with just one force field and consistent parameters, that
is just as important than which kind of force field you pick.
while the hybrid pair styles in LAMMPS are very powerful tools, they
have to be used very carefully and require attention to detail.

axel.

Thanks a lot Axel for calling attention to good ways for choosing a FF. I fully agree: reaxFF is widely used and may be not always right.
Pascal

Ok this is a very important information.
Else may be reaxFF can work ? I am not sure but I think I have seen some attempts.
A good way is to use google scholar with « graphene oxide reaxff » and look at what is proposed.

but look at the background of the people that do the simulations and
the focus of the journal the publication is in. these days, you can
get things published in journals, that don't have simulation/force
field experts as reviewers and thus don't look very carefully at the
specifics of the model (or don't have the skills to tell the
difference between a good and a not so good model).

what is a good choice strongly depends on the properties that one is
interested in. CHARMM or similar "generic" force fields can quite
suitable for some kinds of studies.
ReaxFF offers a much more flexible force field model, but then one has
to be more careful about transferability and the right
parameterization can give a much more accurate results (at
correspondingly higher computational cost). but in both cases, you
would stick with just one force field and consistent parameters, that
is just as important than which kind of force field you pick.
while the hybrid pair styles in LAMMPS are very powerful tools, they
have to be used very carefully and require attention to detail.

axel.