Thank you for the reply, Sorry for the confusion of my two emails. I guess I was using the word "pulling" in the wrong context. Now after my extensive reading, what I meant is that i want to calculate the absoulte binding free energy of a ligand/receptor complex.
I have read the manual over and looked at the tutorials, and came to the idea that i can constrain distances b/w the ligand and the receptor and input a distance for state B to vary the distance using lamda. (Manual 3.3 chapter 6 special topics, section 6.3 Calcuating the PMF using the free-energy code) I am using contraints type 2, which can be perturbed in free energy calculations. here is what I used in my calculation: [ constraints ] ; ai aj funct length_A length_B 44 258 2 0.259 2.406 123 179 2 0.329 2.334 I am currently running a 5ns using the slow-growth method to give me an idea of what happens to the system. I am also looking into using orientational-restrains and using a thermodynamic cycle instead of PMF of the unbinding of the ligand to receptor. please correct me if I am wrong. and thanks for ur help. Belquis > Hi > > First, for the other topic you posted (which is probably somehow related > to this one): > > Now, please be more specific with what you want to do....You wrote: > "What I want to do is calculate the free energy difference of pulling > the ligand away from the receptor" > > This is a pulling approach, where you would like to do AFM sims and > afterwards use Jarzynski. If that is what you want, search the > literature for Jarzynski and try to understand his theorem (you will > see, one pulling sim is not enough for free energy calc). > > Then you wrote: > "I want to do it using theromdynamic intergration using the Lamda 0/1 > stuff" > > This is a totally different approach.... > > With both, you can ESTIMATE binding free energies. Still, both are very > different in the way to setup a simulation in GROMACS. You WILL find > out, how to do it by: > 1. Reading the manual > 2. Searching the mailing list > 3. Using the GROMACS Wiki > 4. Using some of the tutorials, which were posted, by e.g. David Mobley > > Now, coming to your idea about using distance restraints to "pull" the > ligand away (its more of a push). > I think (correct me if I'm wrong), that you can't use A and B state > distance restraints in GROMACS (or better say, they will stay the same > for both states). > > I'd suggest to use either TI OR AFM pulling. For sure, you could do both > and see, if you get similar free energy differences with both methods... > I don't think, you can calculate the free energy difference by using > different distance restraints, anyway. > > Regards > > P.S. > As I just saw it. Inform yourself about the difference between > CONSTRAINTS and RESTRAINTS (there is an important one...) > > Maik Goette, Dipl. Biol. > Max Planck Institute for Biophysical Chemistry > Theoretical & computational biophysics department > Am Fassberg 11 > 37077 Goettingen > Germany > Tel. : ++49 551 201 2310 > Fax : ++49 551 201 2302 > Email : mgoette[at]mpi-bpc.mpg.de > mgoette2[at]gwdg.de > WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ > > > [EMAIL PROTECTED] wrote: >> hello all, >> >> >> is it possible to constrain a distance (or several) between a >> ligand-receptor complex inorder to simulate free energy change of >> separating the ligand from the receptor? >> >> I intend to use TI and lamda to do free energy calculations. >> >> >> any help is appreicated. >> >> Belquis >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> 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 >> >> . >> > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > 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 > > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
