Dear all, I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino acids from its homodimer in opposite directions along z axis. The interfaces of each protein chain is parallel to the z axis. I do not need any restraints in this case. I have gone through the GROMACS manual and some of the previous archived messages and set the following mdp options.
; Pull code pull = yes pull_ngroups = 2 pull_ncoords = 2 pull_group1_name = chain_A pull_group2_name = chain_B ;pull_group3_name = Protein pull_coord1_type = umbrella pull_coord2_type = umbrella pull_coord1_init = 0.0 pull_coord2_init = 0.0 pull_coord1_start = yes ; define initial COM distance > 0 pull_coord2_start = yes pull_coord1_geometry = direction pull_coord2_geometry = direction pull_coord1_groups = 2 1 pull_coord2_groups = 1 2 pull_coord1_dim = N N Y pull_coord2_dim = N N Y pull_coord1_rate = 0.01 ; 0.008 nm per ps = 8 nm per ns pull_coord2_rate = 0.01 ; 0.008 nm per ps = 8 nm per ns pull_coord1_k = 2000 ; kJ mol^-1 nm^-2 pull_coord2_k = 2000 pull_coord1_vec = 0.0 0.0 1.0 pull_coord2_vec = 0.0 0.0 -1.0 nstcalcenergy = 1 nhchainlength = 1 But it fails to pull chain_A in positive z direction. However, chain_B is seemed to pull in negative z direction. Someone please suggest the proper way to pull two groups in opposite directions, or if there is anything that I am missing. waiting for your great help.. Nabajyoti Goswami Bioinformatics Infrastructure Facility Department of Animal Biotechnology College of Veterinary Science Khanapara,Guwahati 781022 Assam, India -- 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.