Hello, What I want to do is calculate the free energy difference of pulling the ligand away from the receptor. I want to do it using theromdynamic intergration using the Lamda 0/1 stuff. I am just not clear of the procedure of how to do it.
I want to constraint several distances between the ligand and the receptor and then increase that distance for state B(lamda=1)where the ligand and receptor are completely separated. For that, I would have to modify my topology where i define [ constraints ] for the distances i want to constrain between the ligand and the receptor and input the bond length for state A(lamda=0) and state B (lamda=1) for each. will the distances defined move the whole ligand away from the receptor? since am only defining several distances between ligand and receptor only. I want to make sure that my procedure above is correct for thermodynamic integeration. hope this clearifies what I am trying to say. Belquis > Sorry, I really didn't get, what your goal is and what, in fact, you > really want to do. > > For free energy calculations, you can > - either do Thermodynamic integration (the lambda 0/1 stuff) > - or pulling (force probe) and afterwards use Jarzynskis theorem > - or umbrella sampling together with WHAM (if I remember correctly) > > Now, it's up to you, which method you favor....may also depend on your > system/question > > Regards > > 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 Gromacs users, >> >> I am trying to do a free energy calculation, which I have never done >> before. I have read the manual and the tutorial on the wiki but there >> is >> still some issues not clear to me. >> >> I am trying to calculate free energy difference of pulling the ligand >> from >> a beta-sheet receptor. I understand there is a pull code with different >> options or it can be done with constraint distances. >> >> Please correct me if my procedure is wrong: I want to constraint >> several >> distances between the ligand and the receptor and then increase that >> distance to one where the ligand and receptor are completely separated. >> For that, I would have to modify my topology where i define [ >> constraints >> ] for the distances i want to constrain between the ligand and the >> receptor and input the bond length for state A(lamda=0) and state B >> (lamda=1) for each. >> >> will the distances defined move the whole ligand away from the >> receptor? >> since am only defining several distances between ligand and receptor >> only. >> >> or is it recommended to use the pull code? >> >> Any directions is appreciated. >> >> 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
