Dear Gromacs users, I am having a very strange problem with "Nose Hoover thermostat with Parrinello-Rahman barostat" NPT simulations for a system of an ion of charge +2 in flexible water molecules. Flexible water is taken from J. Chem. Phys. 124, 024503 (2006); http://dx.doi.org/10.1063/1.2136877. The ion is [UO2]2+ with charge on U=2.5 and each O has -0.25.
Atoms very soon get frozen after the simulation starts and they remain frozen, they do not move at all. Only simulation box oscillates, which causes atoms to oscillate little bit but they do not move at all. Pressure, temperature etc. all get messed up. Here is some output from g_energy: " Statistics over 400001 steps [ 0.0000 through 400.0000 ps ], 3 data sets All statistics are over 40001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Potential -23648.5 20 2891.04 -117.711 (kJ/mol) Temperature 306.684 0.1 108.192 -0.566776 (K) Pressure 538.625 4.4 89041.8 79.925 (bar) " I am using this "Nose Hoover thermostat with Parrinello-Rahman barostat" after a well equilibration configuration obtained with Berendsen's thermostat and barostat. This problem is happening only when Parrinello-Rahman barostat used with Nose Hoover thermostat. I also noted the following observations: If I change either one of the thermostat or barostat with Berendsen, frozen problem disappears. If I change flexible water to rigid water, problem disappears. If my system has no ion, no problem happens. If I play with cut offs, rlist, then also sometimes problem disappears. The problem is independent on the size of box and number of water molecules. As expected, Diffusion constant is very close to zero. Here is my input MDP file: integrator = md dt = 0.001 tinit = 0 nsteps = 400000 nstcomm = 10 pbc = xyz ;constraint_algorithm = lincs ;constraints = all-bonds continuation = yes ; continuing from equilibrated NPT nstxout = 200 nstvout = 50000 nstfout = 0 nstlog = 5000 nstenergy = 2000 nstxtcout = 0 xtc-precision = 1000 nstlist = 10 ns_type = grid rlist = 1.1 coulombtype = PME_switch rcoulomb_switch = 0.6 rcoulomb = 0.9 vdw-type = switch rvdw-switch = 0.6 rvdw = 0.9 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-6 optimize_fft = yes tcoupl = nose-hoover tc-grps = System tau_t = 2 ref_t = 298.15 pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure (in bar) compressibility = 4.5e-5 ; isothermal compressibility, bar^-1 gen_vel = no Any help will be highly appreciated. Please let me know if someone needs any additional information to solve this issue. Thanks, Surya Prakash Tiwari -- 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
