[gmx-users] seg fault with distance restraints - problem in graph
Michael Shirts
mrshirts at stanford.edu
Wed Feb 25 22:39:00 CET 2004
I'm playing around with the distance restraint options in gromacs-3.1.4,
trying to get a better idea of what the results are. I set up a model system
with just two LJ atoms, but it keeps crashing. Included are .top, .mdp, .gro,
and .ndx. I debugged it, and it seems to be having problems setting up the
bonded graph -- looking at the bonded graph, it looks like-
*g = {maxbond = 6, nnodes = 0, nbound = 0, start = 2, end = 0, nedge = 0x0,
edge = 0x0, ishift = 0x0}
Which does not appear to be correct.
When mdrun reaches the line in function ta_disres
ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
it gags, because g (the graph array) isn't set up correctly.
Any suggestions? Am I doing something wrong to get distance restraints set
up?
Thanks,
Michael Shirts
-------------- next part --------------
; ../../runs/LG2/coul/LG2-coul.top created by top_FEize.pl from LG2-s.top on Wed Feb 18 18:47:00 PST 2004
; LG2.top created by ligand_porter.pl Sat Jan 10 13:01:40 PST 2004
#define _FF_GAFF
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon
gaff_1 c3 0.0000 0.0000 A 3.39967e-01 4.57730e-01
[ moleculetype ]
; Name nrexcl
LG2 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB
1 gaff_1 1 LG2 c3 1 0.00000 12.010000 gaff_1 0.0 12.010000
2 gaff_1 1 LG2 c3 2 0.00000 12.010000 gaff_1 0.0 12.010000
[ distance-restraints ]
; ai aj type index type1 low up1 up2 fac
1 2 1 0 2 0.4 0.6 1.5 10.0
[ system ]
Restraint2
[ molecules ]
; Compound #mols
LG2 1
-------------- next part --------------
; VARIOUS PREPROCESSING OPTIONS =
title = MRS
cpp = /usr/bin/cpp
include =
define =
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0
dt = 0.002
nsteps = 5000
; mode for center of mass motion removal =
comm-mode = None
; number of steps for center of mass motion removal =
nstcomm = 0
; 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 =
nstcgsteep = 1000
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 50
nstvout = 50
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 50
nstenergy = 50
; Output frequency and precision for xtc file =
nstxtcout = 0
xtc-precision = 10000
; 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 = grid
; 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 = 0.8
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r = 1
; Method for doing Van der Waals =
vdw-type = Switch
; cut-off lengths =
rvdw-switch = 0.7
rvdw = 0.8
; 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 = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-08
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
Tcoupl = no
; Tcoupl = Nose-Hoover
; Groups to couple separately =
tc-grps = SOL
; Time constant (ps) and reference temperature (K) =
tau_t = 0.1
ref_t = 298
; Pressure coupling =
Pcoupl = no
; Pcoupl = Berendsen
; Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 0.1
compressibility = 4.5e-5
ref_p = 1.01325
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = yes
gen_temp = 298
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 = 1e-07
; Highest order in the expansion of the constraint coupling matrix =
lincs-order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle = 60
; 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 = Simple
; 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 = 1
disre-tau = 0
; Output frequency for pair distances to energy file =
nstdisreout = 50
; 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
; Free energy control stuff =
free-energy = no
;free-energy = yes
init-lambda = 0.00
delta-lambda = 0
sc-alpha = 0
sc-sigma = 0
nstdgdl = 50
-------------- next part --------------
Restrain3
2
1LG2 c3 1 1.089 2.356 2.357 -0.3487 0.1997 -0.6329
1LG2 c3 2 1.338 2.611 2.351 0.0595 0.2956 0.1626
4.00000 4.00000 4.00000
-------------- next part --------------
[ System ]
1 2
[ LG2 ]
1 2
[ SOL ]
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