mohsen ramezanpour wrote:
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!
And your reply was that you can't do umbrella sampling efficiently. So the
natural conclusions is you have to look for alternate methods.
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
If it's not posted on the Gromacs website and you can't find another by
searching the web, probably one doesn't exist. If no one has invested the time
to make your life easier, you'll have to do things that a tutorial author would
otherwise have to do for you: read the manual, read lots of literature, and
define a small test case with a well-defined answer (maybe one that's already
published) to validate your procedure.
-Justin
Thanks in advance for your reply
On Sun, Feb 13, 2011 at 3:55 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@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That said, both of those tutorials are out of date, relying on very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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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> <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 <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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