Thank you very much for the discussion, Lachele!
Actually, I tried to see if there are sites on sugars (and near sugar
binding site on some proteins), where density of ions during the
simulation is higher than in the rest of the box and I didn't see
anything special as I would expect (glycosidic linkage was also my first
idea to check as you propose as well). Thank you for the idea with the
cut-off, I'll try to see if there could be some changes induced by the
increase of cut-off.
Cheers,
Sergey
On 10/05/2010 08:36 PM, Lachele Foley (Lists) wrote:
> If you are certain that your sampling is sufficient for your
> oligosaccharide, then the results you get, in some sense, reflect what
> the force field will do. But, you might still need better sampling.
> In nature, the addition of salt lowers the dielectric constant of the
> water, decreasing the extent to which solvent-separated charges affect
> each other. However, in a typical MD simulation like the one you
> describe, there are no extended effects of the ions on the water or
> the solute (e.g., polarizability). So, the only time the ion would
> have an effect is when it is more-or-less directly associated with the
> glycosidic linkage. I just took a look at an MD of sucrose I happen
> to have, and there isn't a lot of space for water between the atoms
> relevant to the glycosidic linkage. Of course, a 1-6 linkage will be
> a little roomier, if you have one of those. My point is that within
> this sort of simulation, you might need to ensure that you
> sufficiently sample interactions of the ions with the glycosidic
> linkage. You could monitor this by tracking the locations of the ions
> with respect to the linkage. You might also try increasing the
> non-bonded cutoff distance so that the ions' effects are counted more
> often. This latter will slow your simulation, of course. And, in the
> end, you may still find that the lack of polarization is the biggest
> effect.
>
> There have been simulations published recently of carbohydrates in
> ionic liquids. Have you looked at those? They might help you to find
> relevant experimental or computational data for comparison.
>
> :-) Lachele
>
> On Tue, Oct 5, 2010 at 11:07 AM, Sergey Samsonov
> <sergeys.biotec.tu-dresden.de> wrote:
>> Thank you, Lachele!
>>
>> On 10/05/2010 03:36 PM, Lachele Foley (Lists) wrote:
>>> What sort of sampling method did you use? What water model? If you
>>> did not sample sufficiently, then you simply aren't observing enough
>>> simulation to tell. How did you sample (REMD, long simulation, etc.)?
>> I use 20ns MD in a box of TIP3 waters (10 A from the sugar to the box
>> border in xleap). It looks like I sampled sufficiently, at least for
>> dihedrals data.
>>> Whenever possible, you should validate any modeling method against
>>> experimental data that correlates to the sort of simulation you are
>>> doing. Are there no experimental studies at all to use for
>>> comparison?
>> Nothing in respect to ionic strength but the data to compare for
>> sampling is available.
>>> It is possible that the behavior you see is indicative of natural
>>> behavior, though I doubt it is a perfect reflection. If there are
>>> deviations, I would expect them to be related to the absence of
>>> polarizability in the model.
>> Exactly, I also expected that since it could have been more polarized,
>> the charged parts of the molecules would behave a bit differently but it
>> doesn't look like this case.
>>
>> Cheers,
>>
>> Sergey
>>> :-) Lachele
>>>
>>> On Tue, Oct 5, 2010 at 6:00 AM, Sergey Samsonov
>>> <sergeys.biotec.tu-dresden.de> wrote:
>>>> Dear All,
>>>>
>>>> I've been checking, how the flexibility of some saccharides changes (in
>>>> terms of glycosidic linkages dihedrals) depending on ionic strength.
>>>> What I found is that there are neither quantitative, no qualitative
>>>> differences for the effect of ionic strength in the range I used (from 0
>>>> up to quite extreme 5M for NaCl). Do you think this could be explained
>>>> by real physical nature of sugars flexibility or it is rather the force
>>>> field (I used ff03 + GLYCAM06) inability to find such effects as changes
>>>> in flexibility of molecules (or their diffusion constant, which I also
>>>> checked) under different values of ionic strength in solvent?
>>>>
>>>> Thanks in advance and best regards,
>>>>
>>>> Sergey
>>>>
>>>>
>>>>
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Received on Wed Oct 06 2010 - 01:00:03 PDT
