Hi again, I actually figured it out. Turns out, it was a stupid formatting error in the .mdp file. Even though I had it as shown, it didn't read the pull command because it wasn't formatted properly (thought it was still a part of the first line). Sorry guys.
--Johnny > 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 > > > ------------------------------------------------- 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
