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[mohsen ramezanpour]

Dear Dr.Justin

I remember I had read this toturial.
I asked in gmx.groups which method can I select if I want to evaluate
binding free energy?
And the answer was Umbrella Sampling!

Besides,
You recommended using free energy cycles in this gmail
I just wanted to know other toturials.
Please let me know if there are any other
Thanks in advance for your reply


On Sun, Feb 13, 2011 at 3:55 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> I couldn't find any tutorial for doing free energy cycles with gromacs.
>> Then I was forced to select Umbrella sampling,I read your toturial and it
>> was very useful for me.I know it approximately good now.
>> Please let me know if there are any tutorial for free energy cycles.
>> I want to learn how I can do this.
>>
>
> When asking if there are tutorials, you should first check the Tutorials
> page; that's why it exists:
>
> http://www.gromacs.org/Documentation/Tutorials#Free_Energy_Calculations
>
> That said, both of those tutorials are out of date, relying on very old
> Gromacs versions.  The fundamental principles still stand, though.  Read in
> the manual about new .mdp options and new methods for calculating free
> energy.
>
> -Justin
>
>  Thanks in advance for your guidance
>>
>> On Sat, Feb 12, 2011 at 4:50 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    mohsen ramezanpour wrote:
>>
>>        Dear All
>>
>>        I want to evaluate the binding free energy of protein-dryg.
>>
>>        My protein has so many atoms(5000 atoms),it make running too long.
>>        I want to use Umbrella sampling for this.
>>
>>        Can I separate active site of protein (a radious of 3 nm around
>>        of my drug )and do my work on this system?
>>
>>
>>    I would think that such a fractured system would suffer from a
>>    number of unpredictable artifacts.  Protein structure is fairly
>>    sensitive, so you'd have to apply lots of artificial restraints to
>>    preserve geometry, but then what if even small conformational
>>    changes are needed to for the protein to properly bind the drug?
>>
>>    Umbrella sampling is one of the more laborious ways of calculating
>>    binding energies.  Free energy cycles would probably be
>>    significantly more efficient, since you can use a smaller box size
>>    and (in all likelihood) run shorter simulations that still converge.
>>
>>    -Justin
>>
>>
>>        Thanks in advance for your guidances.
>>        Mohsen
>>
>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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