[gmx-users] could not write energies: Invalid argument

[Nguyen Hoang Phuong]

I think you should do minimization your system before run or just turn off
the p coupling.

>
> Dear USERS,
>
> I met two problems with messages:
>
> 1) Fatal error: could not write energies: Invalid argument
>
>
> 2) Warning: pressure scaling more than 1%, mu: 1 1 1.01293
> I belived this could be due to tau_p was too small, but it did not help after increase tau_p to  5.0.
>
> My mdp file is as follows:
>
> integrator = md

>
> ; start time and timestep in ps
>
> tinit = 0.0
>
> dt = 0.002
>
> nsteps = 2000
>
> ; 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
>
> bd-fric = 0
>
> ld_seed = 1993
>
> ;
>
> ; ENERGY MINIMIZATION OPTIONS
>
> ; Force tolerance and initial step-size
>
> emtol = 1; 0.001
>
> emstep = 0.1
>
> ; Max number of iterations in relax_shells
>
> niter = 100
>
> ; 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 = 20
>
> nstvout = 20
>
> nstfout = 0
>
> ; Checkpointing helps you continue after crashes
>
> ;nstcheckpoint = 1000
>
> ; Output frequency for energies to log file and energy file
>
> nstlog = 0
>
> nstenergy = 1
>
> ; 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 = system
>
> ;
>
> ; NEIGHBORSEARCHING PARAMETERS
>
> ; nblist update frequency
>
> nstlist = 1
>
> ; ns algorithm (simple or grid)
>
> ns_type = simple
>
> ; 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 = Cut-off
>
> rcoulomb_switch = 0 ;
>
> rcoulomb = 1.0
>
> ; Dielectric constant (DC) for cut-off or DC of reaction field
>
> epsilon_r = 1
>
> ; Method for doing Van der Waals
>
> vdw-type = 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 = 10
>
> fourier_ny = 10
>
> fourier_nz = 10
>
> ; EWALD/PME/PPPM parameters
>
> pme_order = 4
>
> ewald_rtol = 1e-05
>
> ewald_geometry = 3d
>
> surface_epsilon = 0 ;
>
> optimize_fft = 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 ;
>
> ; Salt concentration in M for Generalized Born models
>
> ;gb_saltconc = 0 ;
>
> ;
>
> ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
>
> ;implicit_solvent = No ;
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>
> ; Temperature coupling
>
> tcoupl = no
>
> ; Groups to couple separately
>
> ;Pressure coupling
>
> Pcoupl = berendsen ;
>
> Pcoupltype = surface-tension
>
> tau_p = 5.0 5.0 ;
>
> compressibility = 4.5e-18 4.5e-1 ;
>
> ref_p = 0.0 2.0 ;
>
> ;
>
> ; Random seed for Andersen thermostat
>
> ;andersen_seed = 815131 ;
>
> ;
>
> ; Type of annealing for each temperature group (no/single/periodic)
>
> annealing = no
>
> ; 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 = no
>
> gen_temp = 120
>
> gen_seed = 173529
>
> ; OPTIONS FOR BONDS
>
> constraints = none
>
> ; 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 = 0.0001
>
> ; Highest order in the expansion of the constraint coupling matrix
>
> lincs_order = 4
>
> ; 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 =
>
> ; 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 = Equal
>
> ; Use sqrt of the time averaged times the instantaneous violation
>
> disre_mixed = no
>
> disre_fc = 1000
>
> disre_tau = 1.25
>
> ; 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) to energy file
>
> nstorireout = 100
>
> ; Dihedral angle restraints: No, Simple or Ensemble
>
> ;dihre = No ;
>
> ;dihre-fc = 1000 ;
>
> ;dihre-tau = 0
>
> ; Output frequency for dihedral values to energy file
>
> ;nstdihreout = 100 ;
>
> ; Free energy control stuff
>
> free_energy = no
>
> init_lambda = 0
>
> delta_lambda = 0
>
> sc-alpha = 0
>
> sc-sigma = 0.3
>
> ; Non-equilibrium MD stuff
>
> acc-grps = ;
>
> accelerate = ;
>
> freezegrps = ;
>
> freezedim = ;
>
> cos-acceleration = 0
>
>
>
> Your advice is greatly appreciated. Thanks
>
> Albert
>
>
> ---------------------------------
> Do you Yahoo!?
> Protect your identity with Yahoo! Mail AddressGuard