[gmx-users] mdrun segmentation fault

[Mark Abraham]

> 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

So that's broken already - you have enormous positive energy and 
infinite forces. Stop there and fix it. Either your starting 
configuration has severe atomic overlaps (go and visualize it with the 
periodic box), or some of your topology is broken (try a box of methanol 
on its own, try the protein in vacuum, try a single acid in vacuum)

Mark

> *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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