Re: Topology and parameters for nitrate and nitrite ion

From: Kenno Vanommeslaeghe (
Date: Tue Jul 02 2013 - 09:17:32 CDT

Putting together a topology for nitrate would be trivial, provided all the
parameters (including Lennard-Jones !) are available, as well as the
charges. If you need help with this procedure, I feel it would be more
appropriate to ask at the "Parameter Set Discussion" CHARMM forum. When
doing so, please cite the source where you found the parameters.

For the record: the "Parameter Set Discussion" forum (but *not* the other
CHARMM forums) is open to all people who use the official CHARMM parameter
set, even if they're not using the CHARMM program. An important exception
to this exception is that we generally won't help with problems with the
parameter set that are *specific* to another software than CHARMM, because
is up to the software developers to ensure compatibility with the
parameter file format. Also, *if* you explicitly mention you're a NAMD
user, then it's possible you'll get a knee-jerk reflex from the other
forum regulars: "go ask the NAMD support channels". Don't be discouraged
by this: if I think your question has merit as a general parameter set
question, I'll do my best to answer it.

On 07/02/2013 10:01 AM, wrote:
> Thanks Dr. Vanommeslaeghe. This discussion has helped a lot. However I have a
> problem which is probably very naive because I have never used OPLS before.
> After searching on the internet, while I am able to find OPLS "parameters" for
> nitrate, I am not able to find something like a topology file. Am i just not
> searching correctly or there is a different way of making psf files for
> molecules not included in the topology file included in the CHARMM force field
> package.
> Any suggestions will be highly appreciated.
> Warm regards.
> Amin.
>> Hi Massimiliano,
>> On 07/01/2013 07:41 AM, Massimiliano Porrini wrote:
>>> In fact, OPLS FF uses a *geometric* combination rule both
>>> for LJ interaction strength (\epsilon) and for size of atoms (\sigma),
>>> whereas CHARMM FFs use Lorentz-Berthelot combining rules, that is
>>> geometric for \epsilon and arithmetic for \sigma.
>> That's an excellent question, thanks for bringing it up. The short answer
>> is that transferring parameters between force fields with different
>> combining rules is generally wrong, and may cause significant deviations
>> in properties. Let's just say that the fact that we *often* get away with
>> it *in the specific case* of OPLS --> CHARMM is just an empirical
>> observation. There's probably a reason for this and I have a good hunch of
>> what it could be, but I don't want to start speculating on this
>> mailinglist. If you want to know for sure, you have to ask my mentor Alex
>> MacKerell.
>>> Is there any workaround about this different way of implementing LJ
>>> parameters?
>> Not that I know of.
>>> For instance: can one somehow specify a \sigma geometric combination rule
>>> only for those atoms for which OPLS FF parameters are implemented?
>> That would leave all the vdW interactions between an "arithmetic" and a
>> "geometric" atom type undefined.
>>> Or it has already been demonstrated that using OPLS LJ parameters
>>> within CHARMM, implementing Lorentz-Berthelot combination rules, is not
>>> harmful for the results of the simulations?
>> Generally spoken, no, but there are a large number of case studies where
>> it gave pretty good results. Assuming the OPLS nitrate parameters Amin
>> spoke of are well-optimized, porting them into CHARMM is almost certainly
>> better than the other options that came up in this discussion thread
>> (short of a big ion parametrization project).
>> > On 1 July 2013 09:52, Kenno Vanommeslaeghe wrote:
>> >> because
>> >> the CHARMM nonbonded parameters are historically based on OPLS ones.
>> I'd like to correct this - I meant or write: "*some* CHARMM nonbonded
>> parameters".
>> Cheers,
>> Kenno.
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