Re: Restraints between ion and small molecule

From: Aron Broom (broomsday_at_gmail.com)
Date: Mon Jul 14 2014 - 21:13:44 CDT

thanks for replying with that, great to have threads that actually have the
last bit of information in them.

On Mon, Jul 14, 2014 at 9:51 PM, Daniel Torrente <danieltorrenteq_at_gmail.com>
wrote:

> Well, I tested differents simulation times (5ns, 10ns and 30ns) under
> differents L-J parameters for the Au+1 and for this system in particular
> the enthalpy stop changing between 5 and 10 ns.
>
> Best regards,
> Daniel
>
> Daniel
>
>
>
> 2014-06-27 8:19 GMT-05:00 Aron Broom <broomsday_at_gmail.com>:
>
> Hi Daniel,
>>
>> I've never actually tested how long the proper sampling would take. My
>> guess would be something in the range of 10 ns. If you end up testing it,
>> maybe toss a reply in here so that others have a better idea.
>>
>> ~Aron
>>
>>
>> On Thu, Jun 26, 2014 at 3:56 PM, Daniel Torrente <xlb608_at_my.utsa.edu>
>> wrote:
>>
>>> Hi Aron,
>>> I know in advance the average distance and the delta H of the
>>> interaction between the gold ion and the ammonia by experiments. I thought
>>> the same as you if I did not restrain the unbound condition, may be the
>>> unrestrained ion could bound to a water molecule during the simulation.
>>> Regarding, the other condition that you propose I think that is a good idea.
>>>
>>> At first I will assume the MM ff values, but I was planning to do a
>>> trial and error method to fit my delta H value with the experimental value
>>> that I have. Is this totally wrong? In terms of simulation time how much
>>> are we talking about (in average) for the enthalpy of the water with each
>>> ion stops changing 10ns, 100 ns or more
>>>
>>> Thanks for your help,
>>>
>>> Daniel
>>>
>>>
>>> On Thu, Jun 26, 2014 at 1:55 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>>>
>>>> In terms of the restraint method, I'm not totally sure this makes sense.
>>>>
>>>> First, there should be no need to restrain the position of the complex,
>>>> so that is fine.
>>>>
>>>> But, in terms of the two conditions: The one should indeed be
>>>> restrained to the bound state as you have it (though one might ask how you
>>>> determined the distance for the bound state?, it's not clear that you would
>>>> know this in advance). But, I think the other condition should be either
>>>> restrained such that the two have a maximum distance, or, should even more
>>>> appropriately be two separate simulations of just the ammonia, and just the
>>>> gold. Because the delta-H should be the bound minus the unbound, and if
>>>> you impose no restraints within a periodic box, there may be bound
>>>> sometimes, and semi-bound others, but will never really be fully unbound.
>>>> I could be missing something though.
>>>>
>>>> Also, you might want to think about how you'll calculate that delta-H.
>>>> The pairwise interaction between the ions is easy enough (assuming, as
>>>> Kenno mentions, that you are willing to accept the MM forcefield values),
>>>> but you also need to account for all the water, which means you either need
>>>> to run the simulation for long enough that the average enthalpy of the
>>>> water with each ion stops changing, or, you need to do a Poisson-Boltzmann
>>>> style of calculation, which I suppose might also be fraught with not
>>>> capturing the quantum effects that will be important in your small charged
>>>> system.
>>>>
>>>> ~Aron
>>>>
>>>>
>>>> On Thu, Jun 26, 2014 at 2:21 PM, Kenno Vanommeslaeghe <
>>>> kvanomme_at_rx.umaryland.edu> wrote:
>>>>
>>>>> On 06/26/2014 02:16 PM, Kenno Vanommeslaeghe wrote:
>>>>>
>>>>>> then I'd have more fate in a QM approach.
>>>>>>
>>>>>
>>>>> I meant "faith" of course.
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Aron Broom M.Sc
>>>> PhD Student
>>>> Department of Chemistry
>>>> University of Waterloo
>>>>
>>>
>>>
>>
>>
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>>
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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