Tanks David Exactly: I`d want to calculate "dG/dl for some particular component of the energy". Why? I did 2 FEPs, so I have two Delta_Gs for a mutations in 2 states: folded and unfolded. Both Delta_Gs are positive values. The difference between them (Delta_Delta_G) is the value I was looking for. This value agrees with experimental value of Delta_G of unfolding between 2 mutant proteins. Now, I want to know what is stabilizing or destabilizing each state with respect the other. Analysis of each component (e.g. Coul-SR:Prot-Prot) is impossible: it happens that Im searching a delta_E of < 10 Kcal between a magnitude of 10E6. So I thought that if I could obtain a <dE/dl> for a component and then integrate them along lambda (TI method), I could get some idea about its magnitude.
Mauricio > Mauricio, > > > That was exactly what I wanted to know. From one hand, because I just > > wanted to know it and, from the other hand, because I think that if I > have > > some idea about how this calculus is carried out, I was able to > estimate a > > Delta_E for some energy components, for example, > Coul-SR:Protein-Protein > > by means of calculating the corresponding <dE/dl> (even when I know > that > > the value is not a state function as stated in the Mark & v Gunsteren > > paper). Maybe I should have started from this point. Is it posible? > > I'm sorry, I have no idea what you're asking here. Are you talking > about trying to calculate a dG/dl for some particular component of the > energy? That doesn't sound useful, to me, since the components > generally are all interdependent. And if you are trying to separate > out the contribution of different components to the total dG/dl, this > would require source code modifications, in general. Again, if you can > be more specific about what exactly you want to do (what problem are > you trying to solve?) people may be able to be more helpful. > > David > > > > > Message: 6 > > > Date: Mon, 6 Nov 2006 10:19:05 -0800 > > > > > Mauricio, > > > > > > I'm somewhat confused by your question and notation. However, I > think > > > the basic answer is something like this: In molecular dynamics, you > > > know the Hamiltonian from which you are sampling; call it H(x,p, > l), > > > where x denotes all of the positions, p the momentums, and l > lambda. > > > This, of course, is closely linked to the potential energy. Anyway, > at > > > any snapshot, you can simply take the derivative dH(x,p,l)/dl, and > you > > > have dH/dl at that snapshot. This is usually straightforward since > you > > > know the dependence of all of the terms in your Hamiltonian on > lambda, > > > so you actually have the functional form for dH/dl as well -- so it > > > just involves taking the appropriate combination of positions, > > > momentums, etc. This is of course all handled internally by the > code. > > > <dH/dl>, then, is just the time-average of dH/dl, which can be > > > evaluated every step by the code. > > > > > > I am not sure if that's helpful at all, as I'm not entirely sure > what > > > problem you're having. After all, whenever you do TI calculations > in > > > GROMACS, the code gives you back dG/dl (or dH/dl, or dA/dl) for > every > > > snapshot in an xvg output file. Are you just confused about how the > > > code gets this (I think I just answered that above), or are you > trying > > > to figure out how to use it? If you're confused about how to use > it, > > > try to ask a question that relates to the specific issue you're > > > confused about. > > > > > > Best wishes, > > > David Mobley > > > UCSF > > > > > > > > > On 11/5/06, Mauricio Sica <[EMAIL PROTECTED]> wrote: > > > > Dear experts > > > > > > > > I am doing FEP (thermodynamic integration method) simulations. > > > > I have a questions about <dH/dl> calculation in GROMACS. > > > > Take in mind equation 3.77 from the GROMACS 3.3 manual. > > > > There, dA/dl is calculated as > > > > > > > > dA/dl = SS{ (dH/dl) exp()dp dq } / SS{ exp()dp dq = <dA/dl>NVT;l > } > > > > > > > > where SS are doble integrals (sorry for the notation). > > > > > > > > My question is: how is (dH/dl) (in the middel-term of the > equation) > > > > calculated? > > > > My idea is that the difference V(L=1)-V(L=0) is calculated for > every > > > time > > > > step (irrespective of the lambda value of the simulation) and > <dG/dl> > > > is > > > > the time average of that difference. > > > > > > > > <dG/dl> = < V(L=1)(i)-V(L=0)(i)/1 > > > > > > > > > Is this correct? > > > > > > > > > > > > Thanks > > > > > > > > > > > > > > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php