From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Nov 11 2014 - 11:19:17 CST
Thanks.
Could you suggest a protocol to validate params for aerial (i.e., triplet,
if that matters) dioxygen in water solution? It is high time (in my view)
to do that. Spending much computer time on (or raw) uncertain basis is
something curious in 2014. It seems to be a situation common to all ff for
MD.
thanks again
francesco
On Tue, Nov 11, 2014 at 6:07 PM, Kenno Vanommeslaeghe <
kvanomme_at_rx.umaryland.edu> wrote:
> I don't have a clear-cut answer to this question, but can offer some food
> for thought:
> http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=25263#
> Post25263
> http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=28502#
> Post28502
> Bottom line is, as always, that it all depends on what kind of accuracy
> you need. I certainly wouldn't use it for any kind of quantitative (e.g.
> free energy) calculation without stringent validation, but if you just want
> qualitative sampling information on a system in which the oxygen does not
> play a central role, a very approximate model that is either based on "OM"
> in toppar_all36_prot_heme.str or OG2D1 in CGenFF may be good enough.
>
>
>
> On 11/11/2014 11:11 AM, Francesco Pietra wrote:
>
>> Hello:
>> My question is about the heroic use of dioxygen data from
>> toppar_all22_prot_heme.str (by zeroing the charges) and
>> par_all27_prot_lipid.rtf for CHARMM36. I refer to free dioxygen in TIP3
>> water solution.
>>
>> With CHARMM36 the "OM" type of previous FF version should be changed. Is
>> the change to "OG2D1" the best compromise?
>>
>> Thanks for advice
>>
>> francesco pietra
>>
>
>
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