I am working with a membrane protein dimer, each monomer being constituted of a single helix. I have already studied the effect of point mutations on the structure and the free energy involved by using FEP. But I have read a paper in which the author has done PMF calculations in order to calculate the free energy of dimerization. In this paper (ref J. Am. Chem. Soc., 2005, 127 (23), pp 8478–8484) the author describes a system that is quite similar to mine, though he uses NAMD to do obtain the trajectories. I have tried gathering some information on this particular method (PMF) in gromacs and have found very little information regarding PFM being used to separate protein dimers or even separating system containing more than a dozen atoms or so. If I understood correctly, I am supposed to pull the two structures apart, and associate a lambda value for each distance I obtain. Well, I am a little bit lost here, since I did not really understand how is the pull code linked with the free energy calculation. I even found the "two argon PMF" tutorial quite confusing, since I do not see how I would obtain a restrain for the monomers in such a big system. So, for now I would like some information on how to obtain this kind of practical information (tutorials, instructions, articles etc). I know everyone is quite busy solving their own problems, so any direction now would help me have more specific doubts so that I can further address this list with more "useful" questions. Thank you Fabrício Bracht _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
