Re: Topology and parameters for nitrate and nitrite ion

Date: Tue Jul 02 2013 - 09:01:19 CDT

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

Any suggestions will be highly appreciated.

Warm regards.

> 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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