> > Maybe it should be obvious, but (a) why are you constraining two > distances, and (b) are you sure your constraints aren't going to muck > with the internal degrees of freedom for the ligand? I would think one > would like to pull the ligand out of the receptor along some > particular direction, but without doing anything to alter its internal > degrees of freedom, or there would be a free energy associated with > changing its internal degrees of freedom that you wouldn't capture in > the PMF calculation. >
I agree with David's comments here. Check out the 'Special Topic' section of the GMX manual. you can either do a pulling simulation or umbrella sampling (where the position and constrain the ligand on some rxn coordinate, in several simulation). The output of such simulatsions is a *.pdo file, which you can then run g_wham on to obtain a PMF. _______________________________________________ gmx-users mailing list [email protected] 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
