Hello Fellow Users, I am trying to pull a DNA molecule. I have fixed one end and trying to pull the other one using this .mdp file.. force output is all zeros. I have tried going through the user-list but have not found any solution yet. I am using gmx-version 4.5.5.
Any idea why is it happening.?? below is the mdp file i am using. Thank you Raghav ############################################################## title = constraint pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 20000 ; 1ns nstcomm = 10 ; Output parameters nstxout = 100 ; every 10 ps nstvout = 100 nstfout = 20 nstxtcout = 20 ; every 1 ps nstenergy = 20 energygrps = DNA Water_and_ions ; Bond parameters constraint_algorithm = lincs lincs_iter = 1 lincs_order = 4 constraints = all-bonds continuation = no ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc_grps = DNA Water_and_ions tau_t = 0.1 0.1 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = yes ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = constraint pull_geometry = distance ; simple distance increase pull_dim = N Y N pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = Fixed pull_group1 = Pull pull_rate1 = 0.001 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 500 ############################################### -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
