From: Daniel Torrente (danieltorrenteq_at_gmail.com)
Date: Mon Jul 14 2014 - 20:51:55 CDT
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.
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.
> On Thu, Jun 26, 2014 at 3:56 PM, Daniel Torrente <xlb608_at_my.utsa.edu>
>> 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,
>> 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
>>> 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
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