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
>> _______________________________________________
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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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
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Received on Wed Mar 23 2011 - 22:30:02 PDT
