Dear all, I simulate pulling experiment with the AFM-option in GROMACS. I calculate the forces from the .pdo file: F = k_c (/spr/ - /pullg/) with F the force, k_c the springconstant. spring is the position of the spring and /pullg/ the position of the pullgroup. after the bond-breakage the forces have a much lower value, but they do not drop to zero. in this picture is one of my force-distance-curves:
http://www.students.uni-mainz.de/schlesie/diplomarbeit/force-distance-curve.JPG My problem is I do not understand why (after the bond-breakage) the mean value of the force is not zero. The simulations are made in vacuum, so there is no friction. When I use a lower the springconstant the distance (/spr/ - /pullg/) gets greater. Greater springconstant yields a lower distance. Has anybody of you an idea why the mean value of the forces does not drop to zero, or have seen anything similar? Thanks for an answer. Thomas _______________________________________________ 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
