Read about the .mdp options pull_pbcatom0 and pull_pbcatom1
-- original message -- Hi everyone, I have a pulling code running on single machine with Gromacs 4.0.7 The systems composes of a surface, a protein and water I pull the protein from the terminal group on the surface laterally. With Gromacs 3.3.3 (on single processors ) the setup works perfectly and generates correct results for pulling positions compared to g_traj... To be able use periodic molecules (for the surface), I switched to gromacs 4.0.7 and I use the "position" option to reproduce the previous v3 results. The problem is that the pullf.xvg gives negative forces... Normally, the pulling force should reach a pseudo-constant level but in my case it just keep going toward minus infinity (unless I cease the run) Also when I checked position of the pulled group I see that the tangent of the displacement-time curve (which is th pulling rate) is also increasing afte. This is bit irrational since the pulling rate is set constant at the first place... For instance, with a pulling rate of 10nm/ns in 1ns you should have displacement of roughly 10nm. Untill 0.4 ns everything looks ok but then (when the peptide moves to the next periodic box) velocity increases and I have a displacement of more 150nm within 1ns... Also, I must say that in the trajectory the increasing velocity of the pulled can be seen clearly with naked-eye. Here is my mdp file; integrator = md nsteps = 1000000 dt = 0.002 nstlist = 40 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstxtcout = 2000 nstlog = 5000 nstenergy = 5000 constraints = hbonds ns_type = grid coulombtype = pme pme_order = 4 fourierspacing = 0.12 rlist = 0.8 rvdw = 0.8 rcoulomb = 0.8 energygrps = DIAM Protein SO tcoupl = berendsen tc_grps = DIAM Protein SOL tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 gen_vel = no Pcoupl = berendsen Pcoupltype = semiisotropic compressibility = 2.5E-8 4.5E-5 tau_p = 1.0 1.0 ref_p = 1.0 1.0 comm_mode = angular comm_grps = DIAM periodic_molecules = yes pbc = xyz ;PULLING pull = umbrella pull_start = yes pull_geometry = position pull_nstxout = 100 pull_nstfout = 100 pull_ngroups = 1 pull_group0 = DIAM pull_group1 = AA1 pull_vec1 = 1.0 0.0 0.0 pull_init1 = 0.0 0.0 0.0 pull_rate1 = 0.01 pull_k1 = 100 -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
