[gmx-users] Enc: 1-4 ineractions in double precision
Justin A. Lemkul
jalemkul at vt.edu
Sat Dec 19 17:05:04 CET 2009
Jessé Nóbrega wrote:
> Hi justin;
>
> I'm grateful for your help, but unfortunately I didn't solve the
> problem. I made a change in my mdp file. This is my mdout.mdp:
>
Have you done sufficient energy minimization? Your simulation is crashing at
step 0, which usually indicates unresolved atomic clashes.
-Justin
> ==============================================================================================================
> ;
> ; File 'mdout.mdp' was generated
> ; By user: jesse (1001)
> ; On host: slayer
> ; At date: Fri Dec 18 16:14:29 2009
> ;
>
> ; VARIOUS PREPROCESSING OPTIONS
> ; Preprocessor information: use cpp syntax.
> ; e.g.: -I/home/joe/doe -I/home/mary/hoe
> include =
> ; e.g.: -DI_Want_Cookies -DMe_Too
> define =
>
> ; RUN CONTROL PARAMETERS
> integrator = md
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.002
> nsteps = 1000000
> ; For exact run continuation or redoing part of a run
> ; Part index is updated automatically on checkpointing (keeps files
> separate)
> simulation_part = 1
> init_step = 0
> ; 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
> ; Friction coefficient (amu/ps) and random seed
> bd-fric = 0
> ld-seed = 1993
>
> ; ENERGY MINIMIZATION OPTIONS
> ; Force tolerance and initial step-size
> emtol = 10
> emstep = 0.01
> ; Max number of iterations in relax_shells
> niter = 20
> ; Step size (ps^2) for minimization of flexible constraints
> fcstep = 0
> ; Frequency of steepest descents steps when doing CG
> nstcgsteep = 1000
> nbfgscorr = 10
>
> ; TEST PARTICLE INSERTION OPTIONS
> rtpi = 0.05
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout = 500
> nstvout = 500
> nstfout = 0
> ; Output frequency for energies to log file and energy file
> nstlog = 100
> nstenergy = 100
> ; 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 = Protein Non-Protein
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 5
> ; ns algorithm (simple or grid)
> ns_type = grid
> ; Periodic boundary conditions: xyz, no, xy
> pbc = xyz
> periodic_molecules = no
> ; nblist cut-off
> rlist = 0.9
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = PME
> rcoulomb-switch = 0
> rcoulomb = 0.9
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r = 1
> epsilon_rf = 1
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> ; cut-off lengths
> rvdw-switch = 0
> rvdw = 1.4
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension = 3.400
> ; Seperate tables between energy group pairs
> energygrp_table =
> ; 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-5
> ewald_geometry = 3d
> epsilon_surface = 0
> optimize_fft = yes
>
> ; IMPLICIT SOLVENT ALGORITHM
> implicit_solvent = No
>
> ; GENERALIZED BORN ELECTROSTATICS
> ; Algorithm for calculating Born radii
> gb_algorithm = Still
> ; Frequency of calculating the Born radii inside rlist
> nstgbradii = 1
> ; Cutoff for Born radii calculation; the contribution from atoms
> ; between rlist and rgbradii is updated every nstlist steps
> rgbradii = 2
> ; Dielectric coefficient of the implicit solvent
> gb_epsilon_solvent = 80
> ; Salt concentration in M for Generalized Born models
> gb_saltconc = 0
> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
> gb_obc_alpha = 1
> gb_obc_beta = 0.8
> gb_obc_gamma = 4.85
> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
> ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
> sa_surface_tension = 2.092
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl = v-rescale
> ; Groups to couple separately
> tc-grps = Protein Non-Protein
> ; Time constant (ps) and reference temperature (K)
> tau-t = 0.1 0.1
> ref-t = 310 310
> ; Pressure coupling
> Pcoupl = berendsen
> Pcoupltype = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau-p = 4 4
> compressibility = 4.5e-5 4.5e-5
> ref-p = 1.0 1.0
> ; Scaling of reference coordinates, No, All or COM
> refcoord_scaling = No
> ; Random seed for Andersen thermostat
> andersen_seed = 815131
>
> ; OPTIONS FOR QMMM calculations
> QMMM = no
> ; Groups treated Quantum Mechanically
> QMMM-grps =
> ; QM method
> QMmethod =
> ; QMMM scheme
> QMMMscheme = normal
> ; QM basisset
> QMbasis =
> ; QM charge
> QMcharge =
> ; QM multiplicity
> QMmult =
> ; Surface Hopping
> SH =
> ; CAS space options
> CASorbitals =
> CASelectrons =
> SAon =
> SAoff =
> SAsteps =
> ; Scale factor for MM charges
> MMChargeScaleFactor = 1
> ; Optimization of QM subsystem
> bOPT =
> bTS =
>
> ; SIMULATED ANNEALING
> ; Type of annealing for each temperature group (no/single/periodic)
> annealing =
> ; Number of time points to use for specifying annealing in each group
> annealing_npoints =
> ; List of times at the annealing points for each group
> annealing_time =
> ; Temp. at each annealing point, for each group.
> annealing_temp =
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
>
> ; OPTIONS FOR BONDS
> constraints = hbonds
> ; Type of constraint algorithm
> constraint_algorithm = LINCS
> ; Do not constrain the start configuration
> continuation = no
> ; Use successive overrelaxation to reduce the number of shake iterations
> Shake-SOR = no
> ; Relative tolerance of shake
> shake-tol = 0.0001
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order = 10
> ; Number of iterations in the final step of LINCS. 1 is fine for
> ; normal simulations, but use 2 to conserve energy in NVE runs.
> ; For energy minimization with constraints it should be 4 to 8.
> lincs-iter = 1
> ; Lincs will write a warning to the stderr if in one step a bond
> ; rotates over more degrees than
> lincs-warnangle = 30
> ; Convert harmonic bonds to morse potentials
> morse = no
>
> ; ENERGY GROUP EXCLUSIONS
> ; Pairs of energy groups for which all non-bonded interactions are excluded
> energygrp_excl =
>
> ; WALLS
> ; Number of walls, type, atom types, densities and box-z scale factor
> for Ewald
> nwall = 0
> wall_type = 9-3
> wall_r_linpot = -1
> wall_atomtype =
> wall_density =
> wall_ewald_zfac = 3
>
> ; COM PULLING
> ; Pull type: no, umbrella, constraint or constant_force
> pull = no
>
> ; NMR refinement stuff
> ; Distance restraints type: No, Simple or Ensemble
> disre = No
> ; Force weighting of pairs in one distance restraint: Conservative or Equal
> disre-weighting = Conservative
> ; Use sqrt of the time averaged times the instantaneous violation
> disre-mixed = no
> disre-fc = 1000
> disre-tau = 0
> ; Output frequency for pair distances to energy file
> nstdisreout = 100
> ; Orientation restraints: No or Yes
> orire = no
> ; Orientation restraints force constant and tau for time averaging
> orire-fc = 0
> orire-tau = 0
> orire-fitgrp =
> ; Output frequency for trace(SD) and S to energy file
> nstorireout = 100
> ; Dihedral angle restraints: No or Yes
> dihre = no
> dihre-fc = 1000
>
> ; Free energy control stuff
> free-energy = no
> init-lambda = 0
> delta-lambda = 0
> sc-alpha = 0
> sc-power = 0
> sc-sigma = 0.3
> couple-moltype =
> couple-lambda0 = vdw-q
> couple-lambda1 = vdw-q
> couple-intramol = no
>
> ; Non-equilibrium MD stuff
> acc-grps =
> accelerate =
> freezegrps =
> freezedim =
> cos-acceleration = 0
> deform =
>
> ; Electric fields
> ; Format is number of terms (int) and for all terms an amplitude (real)
> ; and a phase angle (real)
> E-x =
> E-xt =
> E-y =
> E-yt =
> E-z =
> E-zt =
>
> ; User defined thingies
> user1-grps =
> user2-grps =
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
>
> =========================================================================================================================
>
> When running mdrun, received the following warnings:
>
> =========================================================================================================================
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms nan, max inf (between atoms 721 and 722)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 721 722 90.0 0.1000 inf 0.1000
> 721 723 90.0 0.1000 inf 0.1000
> 721 724 90.0 0.1000 inf 0.1000
> ...
> Warning: 1-4 interaction between 4359 and 4364 at distance inf which is
> larger than the 1-4 table size 4.800 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> Warning: 1-4 interaction between 1195 and 1200 at distance inf which is
> larger than the 1-4 table size 4.800 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> Warning: 1-4 interaction between 4625 and 4630 at distance inf which is
> larger than the 1-4 table size 4.800 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> Warning: 1-4 interaction between 510 and 513 at distance inf which is
> larger than the 1-4 table size 4.800 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> Warning: 1-4 interaction between 4494 and 4499 at distance inf which is
> larger than the 1-4 table size 4.800 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> Warning: 1-4 interaction between 1382 and 1387 at distance inf which is
> larger than the 1-4 table size 4.800 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> Warning: 1-4 interaction between 1061 and 1064 at distance inf which is
> larger than the 1-4 table size 4.800 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> Warning: 1-4 interaction between 4398 and 4403 at distance inf which is
> larger than the 1-4 table size 4.800 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> rank 5 in job 1 slayer_35381 caused collective abort of all ranks
> exit status of rank 5: killed by signal 9
> rank 3 in job 1 slayer_35381 caused collective abort of all ranks
> exit status of rank 3: killed by signal 9
>
> ================================================================================================================================================================================
>
> Please, if it will not disturb you, could you help me how to solve this
> problem?
>
> ------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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