[gmx-users] Gibbs free energy of binding
ramezanpour.mohsen at gmail.com
Wed Oct 20 13:59:40 CEST 2010
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?
On Wed, Oct 20, 2010 at 2:28 PM, Justin A. Lemkul <jalemkul at vt.edu> 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
> 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
> thanks in advance
>> On Tue, Oct 19, 2010 at 2:56 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> 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
>> -- ========================================
>> 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
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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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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