Dear Justin<br><br>If I do two MD simulations for a short time in the same conditions(of course separately for protein and drug)<br> and calculate total energy of each one and sum them with each other as E1 as nonbonding free energy of system.<br>
then a MD simulation for Protein-drug system in the same condition and calculate it's total energy too as E2 as bound system .<br>what does (E1-E2)mean?<br>I think it is binding free energy,Is not it?<br>in the other hand when we are working on NPT ensamble it means Gibbs free energy is the main energy and our total energy is equal to Gibbs free energy.<br>
Then,what is the problem?<br><br><br><br><br><br><div class="gmail_quote">On Wed, Oct 20, 2010 at 3:31 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Justin<br>
You are right,But I searched in tools and I found g_sham<br>
It is very useful tool for estimating Gibbs free energy,Enthalepy ,<br>
emtropy and ...<br>
I think I can use from that for my calculation of binding free energy(In the other words,del G free energy of system )<br>
how do you think about g_sham?<br>
<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
<br>
On Wed, Oct 20, 2010 at 2:28 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
mohsen ramezanpour wrote:<br>
<br>
Dear Gromacs users<br>
<br>
I want to calculate Gibbs free energy too,but about Protein-drug<br>
binding.<br>
Please guide more clearly,what texts I need to read for learning<br>
how can I do it?<br>
<br>
<br>
Look into the literature and nearly any of the popular simulation<br>
textbooks.<br>
<br>
<br>
Besides,g-energy has an option for estimating free energy from<br>
trajectory file(-fee option)<br>
I thought if I had a trajectory file of binding state I could<br>
estimate binding free energy by this option.<br>
am I right?<br>
does it give me Gibbs free energy?(Is this equall to binding<br>
free energy?)<br>
<br>
<br>
Never used this option, but from the description of the option, it<br>
calculates delta(G) relative to an ideal gas state, which sounds<br>
completely unrelated to what you want to accomplish.<br>
<br>
Besides, if g_energy could magically solve this difficult problem,<br>
no one would bother with more thorough methods, like PMF or<br>
thermodynamic integration.<br>
<br>
-Justin<br>
<br>
thanks in advance<br>
Mohsen<br>
<br>
<br>
On Tue, Oct 19, 2010 at 2:56 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div></div><div class="im">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
shahab shariati wrote:<br>
<br>
Hi gromacs users<br>
Can I use gromacs for obtaining Gibbs free energy of<br>
binding of<br>
protein and dna?<br>
<br>
<br>
Yes. I would suggest you read about potential of mean force<br>
calculations.<br>
<br>
-Justin<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
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ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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========================================<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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