Dear Justin, I have been practicing umbrella sampling simulations following your tutorial step by step. I have just finished to perform the pull simulations to identify the configurations to use in the umbrella runs. I have used the distances.pl script to run iteratively g_dist and the resulting file (summary_distances.dat) is showing a distance between 2.62nm (for conf0.gro) and 5.3nm (for conf500.gro). I don't seem to have the values reported in the tutorial at all (in the tutorial is reported that the COM distance would be something of an order of magnitude lowerŠ) and I am not sure if something is gone wrong.
I have also tried to visualize the trajectories but I am not able to see chain_A moving away from the rest of the fibril. I have set, at the end of the topol_Protein_chain_B.itp file, the lines suggested to restrain chain B. #ifdef POSRES_B #include "posre_Protein_chain_B.itp" #endif I have used all the input files given in the tutorial and the commands/files extensions suggested. Can you please help me to understand if I am doing something wrong? Thank you very much for your help. Davide -- 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
