Ian,
Many thanks for the reference. Much appreciated.
Have a good day
George
On Aug 14, 2012, at 10:06 AM, Gould, Ian R wrote:
> Hi George,
>
> You may also wish to take a look at a paper of ours were we tried to
> address some of these issues
> Bradshaw RT, Patel BH, Tate EW, et al <>, Comparing experimental and
> computational alanine scanning techniques
> for probing a prototypical protein-protein interaction., Protein Eng Des
> Sel, 2011, Vol:24, Pages:197-20
>
> doi:10.1093/protein/gzq047
>
> Cheers
> Ian
>
>
> Women love us for our defects. If we have enough of them, they will
> forgive us everything, even our intellects.
> Oscar Wilde,
> --
> Dr Ian R Gould
> Reader in Computational Chemical Biology
> Department of Chemistry
> Imperial College London
> Exhibition Road
> London
> SW7 2AY
> E-mail i.gould.imperial.ac.uk
> http://www3.imperial.ac.uk/people/i.gould
> Tel +44 (0)207 594 5809
>
>
>
>
>
> On 14/08/2012 03:08, "Jason Swails" <jason.swails.gmail.com> wrote:
>
>> On Mon, Aug 13, 2012 at 4:42 PM, George Tzotzos <gtzotzos.me.com> wrote:
>>
>>> Hi everybody,
>>>
>>> I know that there is no prescribed answer to my question but I'd still
>>> like to ask as my computational power is rather limited (running a 24
>>> core
>>> Mac)
>>>
>>> In calculating free energies of binding (MMPBSA) is it preferable to
>>> run a
>>> long trajectory or several smaller ones? I'm dealing with a proteins of
>>> ~150 residues.
>>>
>>
>> Genheden et. al has discussed this point (DOI 10.1002/jcc.21366) and come
>> to the conclusion that several short simulations give rise to more
>> statistically converged answers, since you obtain more uncorrelated
>> structures that way.
>>
>> Of course if you started with the same structure and ran only 10 fs, you
>> would get statistically converged answers as well (in that the standard
>> deviation would be small), since they're all effectively the same
>> structure
>> (and you never know, the various snapshots may even appear uncorrelated :)
>> ). That's obviously not what they did there (they ran ~200 ps per
>> simulation, IIRC), but I'm still not entirely convinced.
>>
>> HTH,
>> Jason
>>
>>
>>> Your experience is valued
>>>
>>> George
>>>
>>>
>>>
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
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>
>
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Received on Tue Aug 14 2012 - 01:30:04 PDT
