Dear Gromacs users, I would like to use the pull code to pull two monomer closer to each other. I am a bit confused on which of the following parameters (in red) needs to have a positive or negative sign to allow the pulling on the same direction. I want to pull the Chain_B, corresponding the one monomer, towards the Chain_A, corresponding to the second monomer. Does anyone perform that before??
; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y ; pull along z pull_group0 = Chain_B pull_group1 = Chain_A pull_vec1 = 0.0 0.0 -1.0 pull_ngroups = 1 ; two groups defining one reaction coordinate pull_start = yes ; define initial COM distance > 0 pull_rate1 = -0.01 ; 0.01 nm per ps = 10 nm per ns due to the minus sign it pulls to opposite direction pull_k1 =1000 ; kJ mol^-1 nm^-2 Many thanks in advance, Regards, Nawel -- Dr Nawel Mele, T: +33 (0) 634443794 (Fr) +44 (0) 7704331840 (UK) -- 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.
