Dear Users: Hello? As you might know, I am trying to simulate polymer chains with gromacs. Thanks to Justin's large help, I can build topology, which is the essential to actually run the MD. After getting the MD result, I have a serious question.
For polymer, as same as the other biopolymers, I assigned potential parameters for 1) bond (stretch), 2) angle, 3) dihedral, 3) improper values. I believe the grompp was working well, because there was no error message at all. After doing a set of actual simulations with my tpr file (and I've checked the processed topology file), unfortunately I could not see any "entanglement" motion. That motion, I believe, should consist of bond, angle, dihedral, improper, as we see in protein simulations. In this case, would you please explain what I have done wrong...? I guessed that the processed force filed (generated by "grompp") could be a problem, but according to Justin's explanations I think it is okay. Please help me! (Hopefully I am becoming more prepared for a real polymer simulation guy...) Thank you! Sincerely, C Kim
_______________________________________________ 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
