[gmx-users] segmentation fault in vanilla TI calculation, death without further noitice

[michael.b]

dear all,

i performed a simple test for free energy calculations
turning off one water molecule to determine the
chemical potential of water.
I start from a well equilibrated water box. At lambda=1.0
(the fully coupled state)  the simulation stops and dies at the
first step without any error messages or warnings. With the other
lambda states (lambda<1.0) things work fine.
I do get a warning from grompp: "For proper sampling of the (nearly)
decoupled
state, stochastic dynamics should be used" which i ignore as the state
lambda=0
is NOT nearly decoupled.

in the log file the energies at step 0 are printed (they look "normal")
then nothing further

stdout is:

[...]
step 0
NOTE: Turning on dynamic load balancing
Segmentation fault (core dumped)

below are my mdp and topology files

any help is appreciated!
thanks,
michael


==================== mdp:

integrator               = md
dt                       = 0.002
nsteps                   = 100000
comm-grps                = System
;
nstxout                  = 100
nstvout                  = 0
nstfout                  = 0
nstlog                   = 100
nstenergy                = 100
;
nstlist                  = 20
ns_type                  = grid
pbc                      = xyz
r_list                   = 1.2
;cutoff-scheme            = Verlet
;
coulombtype              = PME
rcoulomb                 = 1.2
vdw_type                 = cut-off 
rvdw                     = 1.2
DispCorr                 = No
;
tcoupl                   = v-rescale
tc-grps                  = Water few
tau_t                    = 0.2 0.2
ref_t                    = 298.0 298.0
;
gen-vel                  = yes
gen-temp                 = 240.0
gen-seed                 = 45411
;
Pcoupl                   = berendsen 
Pcoupltype               = isotropic
tau_p                    = 0.4
compressibility          = 1.0e-5
ref_p                    = 1.0
;
free-energy              = yes
init-lambda-state        = 10
delta-lambda             = 0
coul-lambdas             = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
vdw-lambdas              = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
calc-lambda-neighbors    = 1
sc-alpha                 = 0.002
sc-r-power               = 48
sc-coul                  = yes
sc-power                 = 1
sc-sigma                 = 0.3

couple-moltype           = few
couple-lambda0           = none
couple-lambda1           = vdw-q
couple-intramol          = no

nstdhdl                  = 100

constraints              = all-bonds
constraint-algorithm     = LINCS
continuation             = no


==================== top:

#define _FF_AMBER
#define _FF_AMBER03

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               2               yes             0.5     0.8333

[ atomtypes ]
; name      at.num  mass     charge ptype  sigma      epsilon
OW           8      16.00    0.0000  A   3.15061e-01  6.36386e-01
HW           1       1.008   0.0000  A   0.00000e+00  0.00000e+00

[ moleculetype ]
; molname       nrexcl
wat             2

[ atoms ]
; id  at type     res nr  res name  at name  cg nr  charge    mass
  1   OW          1       SOL       OW       1      -0.834    16.00000
  2   HW          1       SOL       HW1      1       0.417     1.00800
  3   HW          1       SOL       HW2      1       0.417     1.00800

[ settles ]
; OW    funct   doh     dhh
1       1       0.09572 0.15139

[ exclusions ]
1       2       3
2       1       3
3       1       2

[ moleculetype ]
; molname       nrexcl
few             2

[ atoms ]
; id  at type     res nr  res name  at name  cg nr  charge    mass
  1   OW          1       few       OW       1      -0.834    16.00000
  2   HW          1       few       HW1      1       0.417     1.00800
  3   HW          1       few       HW2      1       0.417     1.00800

[ bonds ]
; i     j       funct   length   force_constant
1       2       1       0.09572  502416.0
1       3       1       0.09572  502416.0
2       3       1       0.15139  502416.0

;[ constraints ]
; 1 2 1
; 1 3 1
; 2 3 1

[ exclusions ]
1       2       3
2       1       3
3       1       2


[ system ]
; Name
w1k

[ molecules ]
; Compound        #mols
wat               999
few                 1


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