[gmx-users] Segmentation fault while running MD simulation

[Justin A. Lemkul]

rainy908 at yahoo.com wrote:
> Hi Justin,
> 
> Sorry I didn't include all of my md.mdp file, as it is quite long :).  I 
> have included as a reference below.  I've taken a look at the log file, 
> but I'm not really sure what I should be looking for so to identify what 
> is causing my system to blow up?  Should I start with the energies (see 
> below)?
>  

Any messages in the log file would be fairly obvious that something is going 
wrong (LINCS warnings, extremely high temperature, energy, etc).

> Finally, I've read through the "Blowing up" link you sent me.  Taking it 
> into consideration, do you suggest that I lower my timestep in my em.mdp 
> file?  It's already at dt = 0.02?
> 

The dt parameter is for MD only; it is irrelevant in EM.  Was EM successful on 
your system?  Have you done any equilibration prior to running unrestrained MD? 
  For the MD, you shouldn't have to reduce the value of dt any further.  20 fs 
is the lowest that the MARTINI developers recommend.

-Justin

> Thanks!
> Lily
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> *log file
> 
> *++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
> Molecular dynamics with coupling to an external bath
> J. Chem. Phys. 81 (1984) pp. 3684-3690
> -------- -------- --- Thank You --- -------- --------
>   
>    Rel. Constraint Deviation:  Max    between atoms     RMS
>        Before LINCS         0.030283    453    454   0.008216
>         After LINCS         0.000040   1278   1276   0.000011
>   
>    Energies (kJ/mol) 
>            Bond       G96Angle        LJ (SR)   Coulomb (SR)      Potential
>     4.22829e+03    7.72020e+03   -6.51083e+06    5.87935e+01   -6.49883e+06
>     Kinetic En.   Total Energy    Temperature Pressure (bar)
>     9.04109e+05   -5.59472e+06    3.10086e+02   -2.18809e+03
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> *md.mdp file*
> 
> 
> integrator               = md
> ; start time and timestep in ps
> tinit                    = 0
> dt                       = 0.020
> ;nsteps                   = 10000 ; initial step
> nsteps                           = 10000000 ; 200 ns @ dt=0.02
> 
> ; number of steps for center of mass motion removal =
> nstcomm                  = 1
> comm-grps                =
> 
> ; OUTPUT CONTROL OPTIONS =
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout                  = 5000
> nstvout                  = 5000
> nstfout                  = 0
> ; Output frequency for energies to log file and energy file =
> nstlog                   = 1000
> nstenergy                = 1000
> ; Output frequency and precision for xtc file =
> nstxtcout                = 10000 ; frame every 150 ps
> xtc_precision            = 1000
> ; This selects the subset of atoms for the xtc file. You can =
> ; select multiple groups. By default all atoms will be written. =
> xtc-grps                 = 
> ; Selection of energy groups =
> energygrps               = PROTEIN W ION
>             
> ; NEIGHBORSEARCHING PARAMETERS =
> ; MARTINI - no need for more frequent updates
> ; or larger neighborlist cut-off due
> ; to the use of shifted potential energy functions.
>    
> ; nblist update frequency =
> nstlist                  = 10
> ; ns algorithm (simple or grid) =
> ns_type                  = grid
> ; Periodic boundary conditions: xyz or none =
> pbc                      = xyz
> ; nblist cut-off         =
> rlist                    = 1.2
> 
> ; OPTIONS FOR ELECTROSTATICS AND VDW =
> ; MARTINI - vdw and electrostatic interactions are used
> ; in their shifted forms. Changing to other types of
> ; electrostatics will affect the general performance of
> ; the model.
> 
> ; Method for doing electrostatics =
> coulombtype              = Shift 
> rcoulomb_switch          = 0.0
> rcoulomb                 = 1.2
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon_r                = 15
> ; Method for doing Van der Waals =
> vdw_type                 = Shift
> ; cut-off lengths        =
> rvdw_switch              = 0.9
> rvdw                     = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure =
> DispCorr                 = No
> 
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
> ; MARTINI - normal temperature and pressure coupling schemes
> ; can be used. It is recommended to couple individual groups
> ; in your system seperately.
> 
> ; Temperature coupling   =
> tcoupl                   = Berendsen
> ; Groups to couple separately =
> tc-grps                  = PROTEIN SOLVENT
> ; Time constant (ps) and reference temperature (K) =
> tau_t                    = 1.0 1.0
> ref_t                    = 310 310
> ; Pressure coupling      =
> Pcoupl                   = berendsen
> Pcoupltype               = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> tau_p                    = 5.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> 
> ; GENERATE VELOCITIES FOR STARTUP RUN =
> gen_vel                  = yes
> gen_temp                 = 310
> gen_seed                 = 1
> 
> ; OPTIONS FOR BONDS     =
> ; MARTINI - for ring systems constraints are defined
> ; which are best handled using Lincs.
> constraints              = none
> ; Type of constraint algorithm =
> constraint_algorithm     = Lincs
> ; Do not constrain the start configuration =
> unconstrained_start      = no
> ; Highest order in the expansion of the constraint coupling matrix =
> lincs_order              = 4
> ; Lincs will write a warning to the stderr if in one step a bond =
> ; rotates over more degrees than =
> lincs_warnangle          = 30
> 

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

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

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