[gmx-users] question in pulling in gromacs 4.0
Hi , I want to pull a molecule from the membrane. My complete mdp file is the following ;. ; File 'mdout.mdp' was generated ; By user: psn (17109) ; On host: p690k ; At date: Fri Jul 23 12:43:31 2004 ; ; VARIOUS PREPROCESSING OPTIONS = title= lipid bilayer in water cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 500 dt = 0.002 nsteps = 175 ; mode for center of mass motion removal = comm-mode= Linear ; number of steps for center of mass motion removal = nstcomm = 1 ; group(s) for center of mass motion removal = comm-grps= ; LANGEVIN DYNAMICS OPTIONS = ; Temperature, friction coefficient (amu/ps) and random seed = ;bd-temp = 300 ;I have commute the above line as it has no exitance bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells = niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints = fcstep = 0 ; Frequency of steepest descents steps when doing CG = nstcgsteep = 1000 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 250 nstenergy= 250 ; Output frequency and precision for xtc file = nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or no = pbc = xyz ; nblist cut-off = rlist= 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME ;Reaction-Field rcoulomb-switch = 0 rcoulomb = 1.0 ;2.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 80.0 epsilon_rf = 1 ;I have done some thing new according to mannual and warnings and error ; Method for doing Van der Waals = vdwtype = Cut-off ; cut-off lengths= rvdw-switch = 0 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = Tcoupl = berendsen ; Groups to couple separately = tc-grps = DPP SOL Na PIP ; Time constant (ps) and reference temperature (K) = tau_t= 0.1 0.1 0.1 0.1 ref_t= 310 310 310 310 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 1.01.0 compressibility = 4.5e-5 4.5e-5 ref_p= 1.01.0 ; SIMULATED ANNEALING CONTROL = annealing= no ; Time at which temperature should be zero (ps) = ;zero-temp_time = 0 ;I have commute the above line as it has no exitance ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 310.0 gen_seed = 173529 ; OPTIONS FOR BONDS = constraints = all-bonds ; Type of constraint algorithm = constraint_algorithm = lincs ; Do not constrain the start configuration = unconstrained-start = no ; Use successive overrelaxation to reduce the number of shake iterations = Shake-SOR= no ; Relative tolerance of shake = shake-tol
Re: [gmx-users] question in pulling in gromacs 4.0
anirban polley wrote: Hi , I want to pull a molecule from the membrane. My complete mdp file snip ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 310.0 gen_seed = 173529 Equilibrate first, then do funky things. Here, in the first step, there is no error or warning during the making of .tpr file.But in the mdrun, after 3/4 steps, it crashes ans stop the MD run. It gives the following error message: Back Off! I just backed up dppc_pip2-ion_NPT_berendsen_md.edr to ./#dppc_pip2-ion_NPT_berendsen_md.edr.2# starting mdrun 'Pure 122 DPPC and 1 PIP2 molecule bilayer with 3592 water molecules' 175 steps, 3500.0 ps. step 0 Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511 Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511 Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511 . t = 500.004 ps: Water molecule starting at atom 10595 can not be settled. Check for bad contacts and/or reduce the timestep. Step 2, time 500.004 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 35.655980, max 638.714233 (between atoms 2849 and 2848) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 943942 54.90.1498 3.0441 0.1530 942941 88.60.1297 0.2327 0.1530 943944 93.10.1291 20.4158 0.1530 944945 93.60.1491 116.4443 0.1530 Wrote pdb files with previous and current coordinates - One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a return 0 or exit(0) in your C code before exiting the application. PID 21625 failed on node n0 (127.0.0.1) due to signal 11. - http://wiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25 Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] question in pulling in gromacs 4.0
anirban polley wrote: ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = Tcoupl = berendsen ; Groups to couple separately = tc-grps = DPP SOL Na PIP ; Time constant (ps) and reference temperature (K) = tau_t= 0.1 0.1 0.1 0.1 ref_t= 310 310 310 310 In addition to Marks' advice, don't couple solvent and ions separately. This is a common error. See here: http://wiki.gromacs.org/index.php/Thermostats -Justin -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
