[gmx-users] segmentation fault

[Justin A. Lemkul]

priya thiyagarajan wrote:
> hello sir,
> 
> thanks for your kind reply..
> 
> in another folder i resubmitted my mdrun from starting time..
> 
> i reduced my time step..
> i kept my time step = 0.001
>  
> 
> this is my md.mdp file
> 
> title        = Gromacs43a1 lipopeptide MD
> ; Run parameters
> integrator    = md        ; leap-frog integrator
> nsteps        = 5000000    ; 1 * 5000000 = 5000 ps, 5 ns
> dt        = 0.001    ; 1 fs
> ; Output control
> nstxout        = 1000        ; save coordinates every 2 ps
> nstvout        = 1000        ; save velocities every 2 ps
> nstxtcout    = 1000        ; xtc compressed trajectory output every 2 ps
> nstenergy    = 1000        ; save energies every 2 ps
> nstlog        = 1000        ; update log file every 2 ps
> ; Bond parameters
> continuation    = yes        ; Restarting after NPT
> 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        = 1.4        ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 1.4        ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.4        ; 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        = DRG   SOL    ; 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 on
> pcoupl        = Parrinello-Rahman    ; Pressure coupling on in NPT
> pcoupltype    = isotropic    ; uniform scaling of box vectors
> tau_p        = 2.0        ; time constant, in ps
> ref_p        = 1.0        ; reference pressure, in bar
> compressibility = 4.5e-5    ; isothermal compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc        = xyz        ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel        = no        ; Velocity generation is off
> 
> 
> i resubmitted my mdrun and my run completed i analysed my output file..
> 
> now it completed at 1.286ns out of 5ns..
> 
> in log file it didnt give any information about this error..
> 
> in error file its showing segmentation fault..
> 
> 
> how to solve this prolem..
> 

Mark already provided this link, but I'll post it again anyway:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

On that page you will find not only several possibilities as to the source of 
the problem, but also the means to diagnose what might be going wrong.  Please 
pay careful attention to this page, as it summarizes this information very well.

> is it only because of some problem in my system??
> 

Yes, quite likely.  The questions that come to mind for me - what is DRG?  What 
is its topology?  Did you do proper energy minimization and equilibration?

-Justin

-- 
========================================

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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