reading your idea:<br>it seems to me I can't ignore entropy contribution because my simulation is at room tempreture.<br>Really I couldn't understand what can I do!<br>I
am working at room tempreture and I want to estimate binding free
energy(delta G),can I ignore entropy in this simulation and calculate
binding free energy by the method that I said in my last email?<br>
what do you think?<br>thank in advance for your guid<br><br><div class="gmail_quote">On Thu, Oct 21, 2010 at 10:45 PM, mohsen ramezanpour <span dir="ltr"><<a href="mailto:ramezanpour.mohsen@gmail.com">ramezanpour.mohsen@gmail.com</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;">reading your idea:<br>it seems to me I can't ignore entropy contribution because my simulation is at room tempreture.<br>
Really I couldn't understand what can I do!<br>I am working at room tempreture and I want to estimate binding free energy(delta G),can I ignore entropy in this simulation and calculate binding free energy by the method that I said in my last email?<br>
what do you think?<br>thank in advance for your guid<div><div></div><div class="h5"><br><br><br><div class="gmail_quote">On Thu, Oct 21, 2010 at 12:15 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</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>On 2010-10-21 10.39, Ehud Schreiber wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Actually, I believe that using the energy difference, Delta E, as an<br>
approximation to the free energy difference, Delta G, is a valid<br>
approach (which I'm considering myself). The entropic contribution to<br>
Delta G, namely -T Delta S, may be less prominent than Delta E.<br>
In addition, Delta S can be approximated by various means - see e.g.<br>
Doig& Sternberg 1995. I understand that such an approach is utilized in<br>
the Accelrys Discovery Studio.<br>
Obviously, this is an approximation that might be too crude for some<br>
applications.<br>
</blockquote>
<br></div>
As a simple example the hydrophobic effect at room temperature is largely due to the entropy of the water [ at high temp it is due to the enthalpy of the water ].<br>
<br>
Since the hydrophobic effect is involved in all ligand binding it seems quite hopeless to get any reliable numbers when neglecting entropy. No referee will buy that - I wouldn't.<div><div></div><div><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
What do you think?<br>
<br>
------------------------------------------------------------------------<br>
--<br>
<br>
On Oct 21, 2010, at 09:25 , Sander Pronk wrote:<br>
<br>
Hi Mohsen,<br>
<br>
The mean energy difference is only one component of the free energy<br>
difference.<br>
<br>
Before you go any further I'd suggest reading a good book on molecular<br>
simulations, like 'Understanding Molecular Simulations' by Frenkel and<br>
Smit.<br>
<br>
There's a good reason free energy calculations cover over half of that<br>
book.<br>
<br>
Sander<br>
<br>
<br>
On Oct 21, 2010, at 09:18 , mohsen ramezanpour wrote:<br>
<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>
<br>
If I do two MD simulations for a short time in the same<br>
</blockquote>
conditions(of course separately for protein and drug)<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
and calculate total energy of each one and sum them with each other<br>
</blockquote>
as E1 as nonbonding free energy of system.<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
then a MD simulation for Protein-drug system in the same condition and<br>
</blockquote>
calculate it's total energy too as E2 as bound system .<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<br>
</blockquote>
free energy is the main energy and our total energy is equal to Gibbs<br>
free energy.<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Then,what is the problem?<br>
</blockquote></blockquote>
<br>
<br>
-- <br></div></div><font color="#888888">
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a></font><div><div></div><div><br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br>
</div></div></blockquote></div><br>