On 17/04/2012 1:50 AM, Laura Leay wrote:
On Fri, 2012-04-13 at 11:01 +1000, Mark Abraham wrote:
On 13/04/2012 2:48 AM, Laura Leay wrote:
All,
I'm trying to run a tabulated soft core potential with the form V =
A + Br^2 + Cr^3 up to about r=0.1 A and the normal LJ 6-12 potential
after this.
I've chosen the parameters of this equation to be the same for all
atoms in my system (a polymer containing carbon, nitrogen and
hydrogen). I've not assigned any charges to the system.
Running on Gromacs version 4.5.4 single precision on a high
perfomance computing cluster the first 50 or so steps run fine,
energies seem reasonable but then the simulation crashes with a
segmentation fault. I submitted the job using the comand mdrun
-table table.xvg -v -nt $NSLOTS -pd
The job seems to run ok on my own desktop PC although I've not tried
running it for more than a few minutes to check that it would indeed
run.
If anyone can tell me why this won't run on the computing cluster
I'd appreciate it.
the first few lines of my table file look like this:
0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00
0.0000000E+00 0.1500000E+05 0.0000000E+00
0.2000000E-02 0.0000000E+00 0.0000000E+00 0.3045913E-01
-0.4568869E+02 0.1499547E+05 0.4525801E+04
0.4000000E-02 0.0000000E+00 0.0000000E+00 0.2436730E+00
-0.1827548E+03 0.1498190E+05 0.9051602E+04
0.6000000E-02 0.0000000E+00 0.0000000E+00 0.8223965E+00
-0.4111982E+03 0.1495927E+05 0.1357740E+05
0.8000000E-02 0.0000000E+00 0.0000000E+00 0.1949384E+01
-0.7310191E+03 0.1492759E+05 0.1810320E+05
0.1000000E-01 0.0000000E+00 0.0000000E+00 0.3807391E+01
-0.1142217E+04 0.1488685E+05 0.2262901E+05
0.1200000E-01 0.0000000E+00 0.0000000E+00 0.6579172E+01
-0.1644793E+04 0.1483707E+05 0.2715481E+05
0.1400000E-01 0.0000000E+00 0.0000000E+00 0.1044748E+02
-0.2238746E+04 0.1477824E+05 0.3168061E+05
0.1600000E-01 0.0000000E+00 0.0000000E+00 0.1559507E+02
-0.2924076E+04 0.1471035E+05 0.3620641E+05
0.1800000E-01 0.0000000E+00 0.0000000E+00 0.2220471E+02
-0.3700784E+04 0.1463341E+05 0.4073221E+05
0.2000000E-01 0.0000000E+00 0.0000000E+00 0.3045913E+02
-0.4568869E+04 0.1454742E+05 0.4525801E+05
0.2200000E-01 0.0000000E+00 0.0000000E+00 0.4054110E+02
-0.5528332E+04 0.1445238E+05 0.4978381E+05
This is my mdp file (note that I turned dispersion correction off to
see if this was the problem but it would seem that it is not):
; VARIOUS PREPROCESSING OPTIONS
title = Yo
cpp = /usr/bin/cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = md ;md for simulation, steep for Emin
; Start time and timestep in ps
tinit = 0
dt = 0.001
nsteps =100000; 1000000 ;for simulation
; 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
; 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 = 100
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (1/ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 0
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 50
nstenergy = 50
; Output frequency and precision for xtc file
nstxtcout = 50
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 =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns_type = simple
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 0.9
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = user
rcoulomb-switch = 0
rcoulomb = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 1
; Method for doing Van der Waals
vdw-type = user
; cut-off lengths
rvdw-switch = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = no ;EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 2.0
; 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 = berendsen
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 300
; Pressure coupling
Pcoupl = no ;berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
; SIMULATED ANNEALING
; 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 = yes
gen_temp = 300
gen_seed = 1993
; OPTIONS FOR BONDS
;constraints = all-bonds
; 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 = 1e-04
; 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 =
You're probably just
http://www.gromacs.org/Documentation/Terminology/Blowing_Up. I suggest
equilibrating with a normal potential, and then shifting to your
special regime. Then you can exclude initial conditions as the source
of the problem, so long as your special regime is not wildly different
from a normal potential.
Mark
The system was first energy minimised without the tabulated potential.
It seems as if it is not blowing up on my desktop PC. Its currently up
to step 4800 (compared to step 50 running on the cluster) and still
going. I'm going to continue to run the job on my desktop PC to see if
it will complete.
The problem definitely seems to lie with the job running on the
computing cluster but I don't know enough about parallel computing etc
to know what the problem is. Any help would be appreciated,
Numerical integration from marginally stable initial conditions can
succeed or fail pretty randomly. See
http://www.gromacs.org/Documentation/Terminology/Reproducibility for
discussion. On the information we have, the hypothesis that running in
parallel causes problems is tenuous. Do you need to use mdrun -pd for
some reason?
Mark
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