David and Berk, I enormously appreciate your help in diagnosing my free energy problems. Berk, when you said "I had implemented the alpha=1 option in 3.3 and set it as default" I presume you mean the sc_power=1 option, yes? David, when you talk of splitting the vdW and charge mutations into separate stages, you mean initially (for example) setting the B-states to have only altered atom types (and hence vdW radii), then later extending the trajectories generated in each window while using a new .top file that also has altered charges in the B-states -- right?
Again, thank you for your help in handling this tricky topic. Matt Ernst Washington State University _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
