Hi there, I have been trying to run a simulation using the fene potential option in a chain of beads as model for my protein, ubiquitin and the sd integrator. The problem comes when one of the beads goes beyond the limits and comes out from the other side of the box, the distance comes out taking into account the position on the other side of the box and not the real one. Therefore my system collapses. Any suggestion on this will be very appreciated.
Marisa Roman Philadelphia, US PS: I could print out coordinates of the beads involved to see the problem: step 970, will finish at Wed Oct 7 13:42:36 2009BONDS: x[42] = (3.533585 2.817612 14.356295 ); x[43] = (3.469475 2.807785 14.618975 ) dr2= 0.0732075 BONDS: x[42] = (3.533310 2.820071 14.356031 ); x[43] = (3.467908 2.807405 14.620831 ) dr2= 0.0745564 BONDS: x[42] = (3.532996 2.822756 14.356280 ); x[43] = (3.466114 2.806527 14.622769 ) dr2= 0.0757529 BONDS: x[42] = (3.532656 2.825698 14.357033 ); x[43] = (3.464116 2.805169 14.624761 ) dr2= 0.0767974 BONDS: x[42] = (3.532295 2.828872 14.358303 ); x[43] = (3.461922 2.803345 14.626786 ) dr2= 0.0776872 BONDS: x[42] = (3.531900 2.832249 14.360102 ); x[43] = (3.459582 2.801082 14.628803 ) dr2= 0.0784018 BONDS: x[42] = (3.531463 2.835809 14.362425 ); x[43] = (3.457096 2.798412 14.630804 ) dr2= 0.0789566 BONDS: x[42] = (3.530972 2.839528 14.365273 ); x[43] = (3.454516 2.795343 14.632739 ) dr2= 0.0793356 BONDS: x[42] = (3.530426 2.843364 14.368648 ); x[43] = (3.451869 2.791898 14.634576 ) dr2= 0.0795378 BONDS: x[42] = (3.529795 2.847286 14.372531 ); x[43] = (3.449184 11.288118 14.636299 ) dr2= 71.3237 ------------------------------------------------------- Program mdrun, VERSION 4.0.5 Source code file: bondfree.c, line: 325 Fatal error: x[42] = (3.529795 2.847286 14.372531 ); x[43] = (3.449184 11.288118 14.636299 ); r^2 (71.323738) >= bm^2 (0.324900) in FENE bond between atoms 43 and 44 ------------------------------------------------------- "The Path Of the Righteous Man is Beset On All Sides With the Iniquities Of the Selfish and the Tyranny Of Evil Men." (Pulp Fiction) _______________________________________________ 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
