mohsen ramezanpour wrote:
Dear Justin
You are right,But I searched in tools and I found g_sham
It is very useful tool for estimating Gibbs free energy,Enthalepy ,
emtropy and ...
I think I can use from that for my calculation of binding free energy(In
the other words,del G free energy of system )
how do you think about g_sham?
It is not applicable. g_sham simply determines free energies based on
histograms of two independent variables. PMF is the appropriate technique for
what you want to do. I can see no other effective way to conduct your study
using Gromacs.
-Justin
On Wed, Oct 20, 2010 at 2:28 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
mohsen ramezanpour wrote:
Dear Gromacs users
I want to calculate Gibbs free energy too,but about Protein-drug
binding.
Please guide more clearly,what texts I need to read for learning
how can I do it?
Look into the literature and nearly any of the popular simulation
textbooks.
Besides,g-energy has an option for estimating free energy from
trajectory file(-fee option)
I thought if I had a trajectory file of binding state I could
estimate binding free energy by this option.
am I right?
does it give me Gibbs free energy?(Is this equall to binding
free energy?)
Never used this option, but from the description of the option, it
calculates delta(G) relative to an ideal gas state, which sounds
completely unrelated to what you want to accomplish.
Besides, if g_energy could magically solve this difficult problem,
no one would bother with more thorough methods, like PMF or
thermodynamic integration.
-Justin
thanks in advance
Mohsen
On Tue, Oct 19, 2010 at 2:56 PM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
shahab shariati wrote:
Hi gromacs users
Can I use gromacs for obtaining Gibbs free energy of
binding of
protein and dna?
Yes. I would suggest you read about potential of mean force
calculations.
-Justin
-- ========================================
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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