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

[Albert Sun]

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


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