[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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