[gmx-users] memory problem (normal mode analysis)
Fabrizio Mancinelli
fabrizio.mancinelli at unina2.it
Mon Feb 6 18:15:30 CET 2006
hi all,
I've got the following error message in performing NMA (recently reported on
this ML):
***
Reading file 4mero_nm.tpr, VERSION 3.3 (double precision)
Loaded with Money
Non-cutoff electrostatics used, forcing full Hessian format.
Allocating Hessian memory...
-------------------------------------------------------
Program mdrun_d, VERSION 3.3
Source code file: smalloc.c, line: 113
Fatal error:
calloc for full_matrix (nelem=280629504, elsize=8, file minimize.c, line 1866)
-------------------------------------------------------
"I'm Your Worst Nightmare" (Creep)
: Cannot allocate memory
***
I have properly (or at least hope so) minimized a 586 residue tetramer (it has
taken about 4 days), and after trying a nm analysis I got the same error
message, even if I'm using the 3.3 version (which is said to use sparse
matrix representation). I have 2Gb of memory.
Maybe something's wrong in my .mdp file, because of which sparse matrix
routine doesn't switch on? I'll paste it on below.
Thanx in advance for any help!
; VARIOUS PREPROCESSING OPTIONS
title = protein
; Preprocessor - specify a full path if necessary.
cpp = /lib/cpp
include = -I../top
define =
; RUN CONTROL PARAMETERS
integrator = nm
; Start time and timestep in ps
tinit = 0
dt = 0.001
nsteps = 500000
; For exact run continuation or redoing part of a run
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 = 0.0001
emstep = 0.0001
; 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 = 10
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 50
nstvout = 100
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; 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 = Protein
; Selection of energy groups
energygrps = Protein
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 0
; ns algorithm (simple or grid)
ns_type = simple
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = no
; nblist cut-off
rlist = 0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Cut-off
rcoulomb-switch = 0
rcoulomb = 0
; Relative dielectric constant for the medium and the reaction field
epsilon-r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdwtype = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; 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-05
ewald_geometry = 3d
epsilon_surface = 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
tc-grps =
; Time constant (ps) and reference temperature (K)
tau-t =
ref-t =
; Pressure coupling
Pcoupl = No
Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 1
compressibility =
ref-p =
; 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 = no
gen-temp = 300
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 = 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, 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-power = 1
sc-sigma = 0.3
; 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
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