Daer Justin I studied your tutorial (Umbrella Sampling). It is very beneficial for me.
The system you considered was the dissociation of a single peptide from the growing end of an protofibril. You considered following parameters: Chain_B: reference group for pulling. Chain_A: group to which pulling force is applied. pulling direction was Z. you placed the center of mass of the protofibril at (3.280, 2.181, 2.4775) in a box of dimensions 6.560 x 4.362 x 12 by editconf: editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12. I have a question: You said " pull distance must always be less than one-half the length of the box vector along which the pulling is being conducted".You pulled a total distance of 5.0 nm in a 12.0-nm box, to avoid the complications described above. Why did you used 2.4775? I think 5.0 is true. Please give me more explanation. How did you obtained this value? Best wishes -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
