Dear Gromacs Users, My system consist of a proteins ( membrane channel) and a drug (DOX) and i am trying to run a pull_md in order to force the drug to permeate the channel, but, the channel size and the durg molecule are closed, so i've been reading , i dont know if i should use constraint to the protein, i think i should in order to facilitated the permeation for my PMF calculation,
i have also read other post about the pulling code i decided to used cylinder like this ; Pull code pull = umbrella pull_geometry = cylinder ; pull_vec1 = 0 0 -1 ; 1 or -1 ?? pull_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = Protein pull_group1 = DOX pull-r1 = 1.0 pull-r0 = 1.0 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 my other question is about the pull-pbcatom1: due to some person presented problems, this should be in the middle of the channel, or select group0 a central atom in the channel , i would really thank all your suggestions and tips, thank you in advance -- View this message in context: http://gromacs.5086.x6.nabble.com/Pulling-code-tp5015320.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
