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 Tue Oct 05 2010 - 08:30:04 PDT
