在 2011-3-24 下午1:11，"Dmitry Nilov" <nilovdm.gmail.com>写道：
> Hi Mahmoud,
> see also reference 130 (Crespo et al., Multiple-steering QM-MM
> calculation of the free energy profile in chorismate mutase) in Amber
> 10 manual to learn more about SMD methodology.
>
> On Thu, Mar 24, 2011 at 2:32 AM, Jason Swails <jason.swails.gmail.com>
wrote:
>> Steered MD and umbrella sampling are two *different* ways of calculating
a
>> PMF along a reaction coordinate. Steered MD is an inherently
>> non-equilibrium driven MD that does not, in general, sample from the true
>> free energy surface. However, Jarzynski's equation relates these
>> non-equilibrium profiles to the true PMF (in a classical stat mech way).
>> Umbrella sampling DOES sample from the true free energy surface (of the
>> hamiltonian modified by a biassing umbrella potential). There are
>> advantages to each over the other, and neither method is particularly
>> cheaper than the other in general.
>>
>> You can find tutorials for steered MD in http://ambermd.org/tutorials/that
>> uses the NCSU functionality. You can also perform steered MD and
umbrella
>> sampling via the NMR restraint facility, but choosing a harmonic shape
for
>> the flat-well potentials. See chapter 6 of the Amber 10 (or Amber 11)
>> manual for instructions on setting up NMR restraints.
>>
>> Hope this helps,
>> Jason
>>
>> On Wed, Mar 23, 2011 at 4:17 PM, Mahmoud Soliman <mahmoudelkot.gmail.com
>wrote:
>>
>>>
>>> Dear amber users,
>>> I wonder can I do PMF calculations for some nucleophilic attack
reaction
>>> in
>>> enzyme using amber 10. I used to do that in dynamo (PMF/umbrella
>>> sampling)
>>> but I am interested to try Amber since it offers higher level methods
>>> (DFTB)
>>> for the QM part which dynamo doesn't. I looked through the tutorials
and
>>> I
>>> found something called streed MD (SMD), is it the same concept? any
other
>>> tutorials/examples I can follow??
>>> Thanks
>>> Mahmoud
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Dmitry Nilov,
> Faculty of Bioengineering and Bioinformatics,
> Lomonosov Moscow State University
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Mar 23 2011 - 22:30:03 PDT
