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
