[gmx-users] segmentation fault during equilibration

[Justin A. Lemkul]

On 5/1/12 1:13 PM, niaz poorgholami wrote:
> thank you Sir for your reply.below I provide you .mdp file:
> title       = UNK-ligand complex NVT equilibration
> define         = -DPOSRES -DPOSRES_LIG 	; position restrain the UNK and LIG
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 50000    ; 2 * 50000 = 100 ps
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout     = 1       ; save coordinates every 0.2 ps
> nstvout     = 1       ; save velocities every 0.2 ps

Your .trr files will be huge with these settings.  I would only recommend 
getting such output every step if your system were collapsing within just a few 
steps, but not in this case.  Though, if you have such output, watching the 
trajectory (provided your workstation doesn't run out of memory) should point to 
the problem.

> nstenergy   = 100       ; save energies every 0.2 ps
> nstlog      = 100       ; update log file every 0.2 ps
> energygrps  = UNK LIG
> ; Bond parameters
> continuation    = no            ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> 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       = 0.9       ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
> rvdw          = 1.4
> ; 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     = UNK_LIG Water_and_ions        ; two coupling groups -
> more accurate
> tau_t       = 0.1   0.1                     ; time constant, in ps
> ref_t       = 300   300
>   ; 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 see nothing particularly glaring with the .mdp file that would be causing a 
problem.  You also did not answer my question about EM, so it is still a 
possibility that the system is insufficiently minimized, but that's just a guess 
since I don't know.

Otherwise: 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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