reading your idea: it seems to me I can't ignore entropy contribution because my simulation is at room tempreture. Really I couldn't understand what can I do! 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? what do you think? thank in advance for your guid
On Thu, Oct 21, 2010 at 10:45 PM, mohsen ramezanpour < ramezanpour.moh...@gmail.com> wrote: > reading your idea: > it seems to me I can't ignore entropy contribution because my simulation > is at room tempreture. > Really I couldn't understand what can I do! > 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? > what do you think? > thank in advance for your guid > > > > On Thu, Oct 21, 2010 at 12:15 PM, David van der Spoel < > sp...@xray.bmc.uu.se> wrote: > >> On 2010-10-21 10.39, Ehud Schreiber wrote: >> >>> Actually, I believe that using the energy difference, Delta E, as an >>> approximation to the free energy difference, Delta G, is a valid >>> approach (which I'm considering myself). The entropic contribution to >>> Delta G, namely -T Delta S, may be less prominent than Delta E. >>> In addition, Delta S can be approximated by various means - see e.g. >>> Doig& Sternberg 1995. I understand that such an approach is utilized in >>> the Accelrys Discovery Studio. >>> Obviously, this is an approximation that might be too crude for some >>> applications. >>> >> >> 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 ]. >> >> 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. >> >> >> >>> What do you think? >>> >>> ------------------------------------------------------------------------ >>> -- >>> >>> On Oct 21, 2010, at 09:25 , Sander Pronk wrote: >>> >>> Hi Mohsen, >>> >>> The mean energy difference is only one component of the free energy >>> difference. >>> >>> Before you go any further I'd suggest reading a good book on molecular >>> simulations, like 'Understanding Molecular Simulations' by Frenkel and >>> Smit. >>> >>> There's a good reason free energy calculations cover over half of that >>> book. >>> >>> Sander >>> >>> >>> On Oct 21, 2010, at 09:18 , mohsen ramezanpour wrote: >>> >>> Dear Justin >>>> >>>> If I do two MD simulations for a short time in the same >>>> >>> conditions(of course separately for protein and drug) >>> >>>> and calculate total energy of each one and sum them with each other >>>> >>> as E1 as nonbonding free energy of system. >>> >>>> then a MD simulation for Protein-drug system in the same condition and >>>> >>> calculate it's total energy too as E2 as bound system . >>> >>>> what does (E1-E2)mean? >>>> I think it is binding free energy,Is not it? >>>> 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. >>> >>>> Then,what is the problem? >>>> >>> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Dept. of Cell & Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >> sp...@xray.bmc.uu.se http://folding.bmc.uu.se >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> 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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >
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