On 8/11/17 5:02 PM, Daniel Kozuch wrote:
Hello, I am using a pull code to increase the end-to-end distance of a protein (included below). I am using direction-periodic and would like the distance between the COM groups to be calculated in three dimensions. However, setting pull_coord1_dim = Y Y Y appears to have no effect and the distance printed to the pull file is still only in the pull_vec dimension (as verified by checking with gmx distance). Is there any way to use pull_coord1_dim = Y Y Y with direction-periodic?
No, because direction and direction-periodic only use pull_coord1_vec. http://manual.gromacs.org/documentation/2016.3/user-guide/mdp-options.html#com-pulling -Justin
pull = yes pull_ngroups = 2 pull_ncoords = 1 pull_group1_name = Chain_Begin pull_group2_name = Chain_End pull_coord1_type = umbrella ; harmonic biasing force pull_coord1_geometry = direction-periodic pull_coord1_groups = 1 2 pull_coord1_dim = Y Y Y pull_coord1_rate = 0.0 pull_coord1_k = 5000 ; kJ mol^-1 nm^-2 pull_coord1_start = no ; define initial COM distance > 0 pull_coord1_init = 3.5 pull_coord1_vec = 0 0 1 Thanks, Dan
-- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
