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<style>.hmmessage P{margin:0px;padding:0px}body.hmmessage{FONT-SIZE: 10pt;FONT-FAMILY:Tahoma}</style>Dear Gromacs Users,<br><br>I am using the most recent version 3.3.99. Iran my simulation with 20ns period for a total length of 300ns so thatI don't have to start from scratch if I have a unexpected crash duringthe simulation. It suppose to write out full precision trr file at theend of every 20ns for the next 20ns to start with. But I the trr filesI got are EMPTY!!<br>Does anyone have any idea about this problem? mdp file is attached. Please help. Thanks in advance. <br><br>Ranqi<br><br>PS: I also encounter unexpected crash with V3.3.99. No error message found.<br><br>This is my mdp file :<br><br>; 20ns NPT production<br>integrator = sd<br>ld_seed = -1<br>; start time and timestep in ps<br>tinit = 0<br>dt = 0.002<br>nsteps = 10000000<br>; number of steps for center of mass motion removal =<br>nstcomm = 100<br>; OUTPUT CONTROL OPTIONS<br>; Output frequency for coords (x), velocities (v) and forces (f) =<br>nstxout = 0<br>nstvout = 0<br>nstfout = 0<br>; Output frequency for energies to log file and energy file<br>nstlog = 50000 ; every 100 ps<br>nstenergy = 50000<br>; Output frequency and precision for xtc file<br>nstxtcout = 50000 ; every 100 ps<br>xtc-precision = 10000<br>xtc_grps = protein other<br>energygrps = protein other<br>; NEIGHBORSEARCHING PARAMETERS<br>; nblist update frequency =<br>nstlist = 10<br>; ns algorithm (simple or grid)<br>ns_type = grid<br>; Periodic boundary conditions: xyz or none<br>pbc = xyz<br>; nblist cut-off<br>rlist = 1.0<br>domain-decomposition = no<br>; OPTIONS FOR ELECTROSTATICS AND VDW<br>; Method for doing electrostatics<br>coulombtype = pme<br>;rcoulomb-switch = 0<br>rcoulomb = 1.0<br>; Dielectric constant (DC) for cut-off or DC of reaction field<br>epsilon-r = 1<br>; Method for doing Van der Waals<br>vdw-type = switch<br>; cut-off lengths<br>rvdw = 0.9<br>rvdw-switch = 0.8<br>; Apply long range dispersion corrections for Energy and Pressure<br>DispCorr = EnerPres<br>; Spacing for the PME/PPPM FFT grid<br>fourierspacing = 0.1<br>; FFT grid size, when a value is 0 fourierspacing will be used =<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>; EWALD/PME/PPPM parameters =<br>pme_order = 6<br>ewald_rtol = 1e-06<br>epsilon_surface = 0<br>optimize_fft = no<br>; OPTIONS FOR TEMPERATURE COUPLING<br>tc_grps = protein other<br>tau_t = 1.0 1.0 ; Langevin friction constant (ps)<br>ref_t = 300 300<br>;OPTIONS FOR PRESSURE COUPLING<br>Pcoupl = berendsen<br>pcoupltype = isotropic<br>tau_p = 5.0 5.0<br>compressibility = 4.5e-05<br>ref_p = 1.0 1.0<br>; GENERATE VELOCITIES FOR STARTUP RUN<br>gen_vel = no<br>; Dielectric constant (DC) for cut-off or DC of reaction field<br>epsilon-r = 1<br>; Method for doing Van der Waals<br>vdw-type = switch<br>; cut-off lengths<br>rvdw = 0.9<br>rvdw-switch = 0.8<br>; Apply long range dispersion corrections for Energy and Pressure<br>DispCorr = EnerPres<br>; Spacing for the PME/PPPM FFT grid<br>fourierspacing = 0.1<br>; FFT grid size, when a value is 0 fourierspacing will be used =<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>; EWALD/PME/PPPM parameters =<br>pme_order = 6<br>ewald_rtol = 1e-06<br>epsilon_surface = 0<br>optimize_fft = no<br>; OPTIONS FOR TEMPERATURE COUPLING<br>tc_grps = protein other<br>tau_t = 1.0 1.0 ; Langevin friction constant (ps)<br>ref_t = 300 300<br>;OPTIONS FOR PRESSURE COUPLING<br>Pcoupl = berendsen<br>pcoupltype = isotropic<br>tau_p = 5.0 5.0<br>compressibility = 4.5e-05<br>ref_p = 1.0 1.0<br>; GENERATE VELOCITIES FOR STARTUP RUN<br>gen_vel = no<br>; Dielectric constant (DC) for cut-off or DC of reaction field<br>epsilon-r = 1<br>; Method for doing Van der Waals<br>vdw-type = switch<br>; cut-off lengths<br>rvdw = 0.9<br>rvdw-switch = 0.8<br>; Apply long range dispersion corrections for Energy and Pressure<br>DispCorr = EnerPres<br>; Spacing for the PME/PPPM FFT grid<br>fourierspacing = 0.1<br>; FFT grid size, when a value is 0 fourierspacing will be used =<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>; EWALD/PME/PPPM parameters =<br>pme_order = 6<br>ewald_rtol = 1e-06<br>epsilon_surface = 0<br>optimize_fft = no<br>; OPTIONS FOR TEMPERATURE COUPLING<br>tc_grps = protein other<br>tau_t = 1.0 1.0 ; Langevin friction constant (ps)<br>ref_t = 300 300<br>;OPTIONS FOR PRESSURE COUPLING<br>Pcoupl = berendsen<br>pcoupltype = isotropic<br>tau_p = 5.0 5.0<br>compressibility = 4.5e-05<br>ref_p = 1.0 1.0<br>; GENERATE VELOCITIES FOR STARTUP RUN<br>gen_vel = no<br>; OPTIONS FOR BONDS<br>constraints = hbonds<br>; Type of constraint algorithm<br>constraint-algorithm = Lincs<br>; Do not constrain the start configuration<br>unconstrained-start = yes<br>; Relative tolerance of shake<br>shake-tol = 0.0001<br>; Highest order in the expansion of the constraint coupling matrix<br>lincs-order = 12<br>; Lincs will write a warning to the stderr if in one step a bond<br>; rotates over more degrees than =<br>lincs-warnangle = 30<br><br /><hr />Reveal your inner athlete and share it with friends on Windows Live. <a href='http://revealyourinnerathlete.windowslive.com?locale=en-us&ocid=TXT_TAGLM_WLYIA_whichathlete_us' target='_new'>Share now!</a></body>
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