Dear all, i have with Gromacs 3.3.3 problem with the afm-pulling (the velocity are not correct) My system consists of ureas with short alkane linkers (see picture below)
+___+___+ | | | x x x x x x | | | ____*____ x are the ureas (which form hbonds), | are the linkers and _ are constraints and distance restraince (so that the molecules have a nearly constant distance). * is the REF-group and + are the PULL-groups. The initial position of the three spring was at the position of the three PULL-groups. For the pull direction i took the vector between the REF-group and the middle PULL-group (and normalized the vector). The pull-direction for the other two PULL-groups was the same (so the pulling of the three molecules should be parallel). For all springs i took the same velocity and spring constant. From the *.pdo i calculeted the distance which the springs moved, and from a plot distance against time i can calculate the velocity. And here comes the problem: the velocity should be 10E-4 nm/ps For the middle spring it was: 9.995E-5 nm/ps (here i think is a small rounding error, due to the normalisation) But for one of the outer springs it was: 7.6939E-5 nm/ps ; additionally the velocity wasn't realy constant, the fit with an polynom (2end order) was much better: 6.9173E-5 (for the linear term) and 6.4715E-10 (for the quadratic term). In a simulation with 15 parallel molecules the decrease of the pulling-velocity was even more extrem. The velocity of the outter most springs was more then 5 times small then the velocity i have writen in the *.ppa file. Has anybody an idea from what this problem arises? Thanks for answers. 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
