Dear All
As explained in the previous post, I’ve faced difficulty to assign force field parameters and partial charges to a heavy hydrocarbon molecule, called Asphaltene, appeared below:
I could not find appropriate parameters for fused carbons in aromatic rings. So, what should I do?
Has anybody experienced such case?
Sincerely
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Dear All
As explained in the previous post, I've faced difficulty to assign force
field parameters and partial charges to a heavy hydrocarbon molecule,
called Asphaltene, appeared below:I could not find appropriate parameters for fused carbons in aromatic
rings. So, what should I do?
a quick search with google shows, that MD simulations on asphaltene
molecules (please note, that this is a *class* of molecules, not a specific
one) have been done. i suggest you read those and follow what is given in
one of the corresponding papers' methods sections.
axel.
Thanks Alex
Really, I’m following rout of other researchers by using well-known force fields, such as OPLS-AA.
However, asphaltene molecule is so complex to incorporate all atom types offered by any force field.
Is it mandatory to use both “vdW parameters” and “partial charges”?
I think it would be necessary to calculate the partial charge of asphaltene atoms through Gaussian software and then specify vdW parameters. Is it correct?
In other words, for such molecules having apparently different atom types, how should I assign force field parameters and partial charges?
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Thanks Alex
Really, I'm following rout of other researchers by using well-known force
fields, such as OPLS-AA.
However, asphaltene molecule is so complex to incorporate all atom types
offered by any force field.
so are you saying, you did *not* look up what people that actually *have*
done in simulations of alphaltene class molecules were using? why not?
Is it mandatory to use both "vdW parameters" and "partial charges"?
I think it would be necessary to calculate the partial charge of
asphaltene atoms through Gaussian software and then specify vdW parameters.
Is it correct?
not directly. if you have to ask these questions, you need to learn more
about force fields, how they are designed, and how parameters are obtained
before you continue. a *lot* more. OPLS-AA for example follows primarily
and increment system to assign parameters. if you stray from that or need
to come up with your own atom times and partial charges, you will have to
spend a *significant* amount of time to *verify* those parameters.
remember, that you need parameters for a system in solution (and a protic
and highly polar (and polarizable) solvent to boot where you have to keep
the averaged effects of your solvent at the given temperature under
consideration). so it is not likely going to be that you just do one
gaussian run and magically obtain the numbers you need. force field
parameterization of new atom types can be tricky and time consuming and is
a bit of black art.
In other words, for such molecules having apparently different atom types,
how should I assign force field parameters and partial charges?
i cannot explain this in an e-mail. there a *lots* of papers (and even
text books) explaining how parameters are obtained (e.g. for multiple
revisions of Amber, CHARMM, OPLS, Gromos, and many more). both Amber and
CHARMM also offer "generalized" force field parameterizations, that are
less accurate but consistent with properly parameterized molecule fragments
of either Amber or CHARMM, respectively.
at any rate, the important next step, that you have to follow is to improve
your understanding of force fields. you should not continue without the
proper understanding. if you cannot find a properly documented and tested
strategy to assign atom types and partial charges, then you need to find a
competent collaborator.
axel.
