[gmx-users] core dumped

Justin Lemkul jalemkul at vt.edu
Sat Dec 27 17:47:04 CET 2014



On 12/27/14 11:42 AM, elham tazikeh wrote:
> Dear users
> when i simulated Aspirin on Human serum albumin (pdb: 2i30)
> in equilibration process (NVT), i encountered with below message and my
> simulation stopped. i dont know why?
>

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

A seg fault leaves nothing to diagnose.  Follow the advice in that link.

-Justin

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> *pdfco at pdfco-X:~/Aspirin$ tail nvt.job-nex         int    0       Number of
> random exchanges to carry out each                            exchange
> interval (N^3 is one suggestion).  -nex                            zero or
> not specified gives neighbor replica
> exchange.-reseed      int    -1      Seed for replica exchange, -1 is
> generate a seed-[no]ionize  bool   no      Do a simulation including the
> effect of an X-Ray                            bombardment on your system*
>
>
>
> *Reading file nvt.tpr, VERSION 4.6.5 (single precision)Using 1 MPI
> thread[1]+  Segmentation fault      (core dumped) mdrun -v -deffnm nvt &>
> nvt.job*
>
>
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>
> my *NVT.mdp* content was:
>
> title  = Protein NVT equilibration
> define  = -DPOSRES             ; position restrain the protein
> ; Run parameters
> integrator = md               ; leap-frog integrator
> nsteps  = 100000      ; 0.002 * 100000 = 200 ps
> dt      = 0.002              ; 2 fs
> ; Output control
> nstxout  = 1000              ; save coordinates every 0.2 ps
> nstvout  = 1000              ; save velocities every 0.2 ps
> nstenergy = 1000              ; save energies every 0.2 ps
> nstlog  = 1000              ; update log file every 0.2 ps
> ; 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  = 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
> tc-grps  = Protein_SAL SOL_CL ; two coupling groups - more accurate
> tau_t  = 0.1 0.1             ; time constant, in ps
> ref_t  = 310  310             ; reference temperature, one for each group,
> in K
> ; Pressure coupling is off
> pcoupl  = no               ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc  = XYZ
> ; 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 really appriciate for your hint
>
> regards
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================


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