[gmx-users] mdrun segmentation fault

[shivangi nangia]

Hello gmx users,

My system for NVT equilbration runs into segmentation fault as soon as I try
to run it.
It does not give any warning or hint of what might be going wrong.
Since I am a new user I am having difficulty exploring the plausible
reasons.

System: Protein( polyhistidine), 20  2,5-dihydroxybenzoic acid anions, 1:1
water: methanol (~3000 molecules of each) in 8 nm cube


I had had EM of the system using steepest decent. Outcome:

Steepest Descents converged to machine precision in 15 steps, but did not
reach the requested Fmax < 1000.
Potential Energy  =  1.5354981e+19
Maximum force     =            inf on atom 651
Norm of force     =            inf

*The minim.mdp *is:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep     ; Algorithm (steep = steepest descent minimization)
emtol    = 1000.0    ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep          = 0.02          ; Energy step size
nsteps      = 50000     ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist     = 1      ; Frequency to update the neighbor list and long range
forces
ns_type     = grid      ; Method to determine neighbor list (simple, grid)
rlist    = 1.0    ; Cut-off for making neighbor list (short range forces)
coulombtype = PME    ; Treatment of long range electrostatic interactions
rcoulomb = 1.0    ; Short-range electrostatic cut-off
rvdw     = 1.0    ; Short-range Van der Waals cut-off
pbc      = xyz       ; Periodic Boundary Conditions (yes/no)
constraints = none




*The nvt.mdp*:

title    = hist NVT equilibration
define      = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md     ; leap-frog integrator
nsteps      = 50000     ; 2 * 50000 = 100 ps
dt    = 0.002     ; 2 fs
; Output control
nstxout     = 100    ; save coordinates every 0.2 ps
nstvout     = 100    ; save velocities every 0.2 ps
nstenergy   = 100    ; save energies every 0.2 ps
nstlog      = 100    ; update log file every 0.2 ps
; Bond parameters
continuation   = no     ; first dynamics run
constraint_algorithm = lincs  ; holonomic constraints
constraints = none ;
lincs_iter  = 1      ; accuracy of LINCS
lincs_order = 4      ; also related to accuracy
; Neighborsearching
ns_type     = grid      ; search neighboring grid cells
nstlist     = 5      ; 10 fs
rlist    = 1.0    ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0    ; short-range electrostatic cutoff (in nm)
rvdw     = 1.0    ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME    ; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4      ; cubic interpolation
fourierspacing = 0.16      ; grid spacing for FFT
; Temperature coupling is on
tcoupl      = V-rescale ; modified Berendsen thermostat
tc-grps     = Protein Non-Protein   ; two coupling groups - more accurate
tau_t    = 0.1 0.1   ; time constant, in ps
ref_t    = 300    300   ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl      = no     ; no pressure coupling in NVT
; Periodic boundary conditions
pbc      = xyz    ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = yes    ; assign velocities from Maxwell distribution
gen_temp = 300    ; temperature for Maxwell distribution
gen_seed = -1     ; generate a random seed


I tried to decrease the step size, that also runs into seg fault error.


Kindly guide.

Thanks,
SN
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