Hello all, how are you doing today? I've been trying to get a stable DNA MD simulation to work for me, but I think my problem lies in an insufficiently energy minimized system prior to running the pr step. I'm using the ffamber99 force field and I've successfully simulated many ns of MD using the sample Dickerson dodecamer pdb file supplied on the gromacs web site. However, when I build my own 21mer using NAB (http://casegroup.rutgers.edu/nab.html), I always get LINCS warnings during the first thousand steps of pr... Here are my settings for em:
define = -DFLEXIBLE constraints = none integrator = steep dt = 0.001 ; ps ! nsteps = 4000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.08 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 8 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 10000.0 emstep = 0.01 here's a sample of the em output: (27 steps sounds awfully short...) Steepest Descents converged to Fmax < 10000 in 27 steps Potential Energy = -3.4305819e+05 Maximum force = 5.8583452e+03 on atom 495 Norm of force = 3.0654459e+02 And here are my settings for pr: define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 20000 ; total 20.0 ps. nstcomm = 1 nstxout = 250 ; collect data every 0.5 ps nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.08 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 8 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529 and here's the output from the failed pr after about 500 steps: ------------------------------------------------------- Program mdrun, VERSION 4.0.5 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1000) If you know what you are doing you can adjust the lincs warning threshold in you r mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem ------------------------------------------------------- Thanks again for all your help! You folks are lifesavers! All suggestions are welcome! Dave Crosby UC Irvine, dept of pathology and laboratory medicine _______________________________________________ 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/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/mailing_lists/users.php