Hi Justin, Thx for the reply. By pull apart, I just wanted to expose an 'activation site' by using a force. It is somewhat similar to pulling two domains of a protein away from each other. I'm not aiming to undo any secondary structure. I hope this is clearer. Thanks again!
--Johnny > > > Johnny Lam wrote: >> Hi again, >> >> >> I am trying to pull apart a CG protein (to verify CG results with those >> of >> already published works using atomistic MD). Using the previous >> suggestions, my new pull code is the following: >> > > By "pull apart," do you mean to unwind the secondary structure of the > protein? > If so, I don't think it will work. Doesn't MARTINI fix certain backbone > parameters such that secondary structure remains very rigid over time? > > If that's the case, then the vibrations you're seeing are just the > structure > trying to resist being pulled apart. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > ------------------------------------------------- Johnny Lam ISPE Berkeley Chapter External Vice President Department of Bioengineering College of Engineering University of California, Berkeley Tel: (408) 655- 6829 Email: john...@berkeley.edu _______________________________________________ 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
