[gmx-users] could not write energies: Invalid argument
Albert Sun
albert_sun9 at yahoo.com
Tue Dec 16 17:09:01 CET 2003
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20031216/a62b3341/attachment.html>
More information about the gromacs.org_gmx-users
mailing list