[gmx-users] Segmentation fault while running MD simulation
rainy908 at yahoo.com
rainy908 at yahoo.com
Sat Nov 14 00:46:08 CET 2009
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)?
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?
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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2009/11/13 Justin A. Lemkul <jalemkul at vt.edu>
>
>
> rainy908 at yahoo.com wrote:
>
>> Hi all,
>>
>> I've encountered a problem while trying to run Gromacs on my
>> coarse-grained molecule. I've already performed the initial energy
>> minimization. I tried to run the inital MD simulation, but the job was cut
>> short due to a segmentation fault, as mentioned in the output file:
>>
>> ^Mstep 0^Mstep 100, will finish Wed Dec 16 16:55:17 2009^Mstep 200, will
>> finish Wed Dec 16 07:04:11 2009^Mstep 300, will finish Wed Dec 16 12:59:33
>> 2009^Mstep 400, will finish Wed Dec 16 09:02:03 2009^Mstep 500, will finish
>> Wed Dec 16 12:12:01 2009^Mstep 600, will finish Wed Dec 16 14:18:47
>> 2009^Mstep 700, will finish Wed Dec 16 15:49:22 2009^Mstep 800, will finish
>> Wed Dec 16 13:29:16 2009^Mstep 900, will finish Wed Dec 16 14:45:15
>> 2009^Mstep 1000, will finish Wed Dec 16 15:46:03 2009
>>
>> /opt/gridengine/default/spool/
>> compute-0-7/job_scripts/182710: line 28: 18851 Segmentation fault
>> (core dumped) $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr -c
>> confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr
>> /opt/gridengine/default/spool/compute-0-7/job_scripts/182710: line 31: -s:
>> command not found
>>
>> Does anyone know what could be causing the problem? Should it be of
>> interest, my em.mdp is included at the bottom.
>>
>> Thanks for your help!
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> em.mdp
>> ; VARIOUS PREPROCESSING OPTIONS =
>> title =
>> cpp = /lib/cpp
>> include =
>> define =
>>
>> ; RUN CONTROL PARAMETERS =
>> integrator = steep
>> ; start time and timestep in ps =
>> tinit = 0
>> dt = 0.02
>> nsteps = 1000
>>
>> ; ENERGY MINIMIZATION OPTIONS =
>> ;emtol = 0.00001
>> ;emstep = 0.1
>> ;nstcgsteep = 1000
>>
>> emtol = 10
>> emstep = 0.01
>> nstcgsteep = 1000
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>> md.mdp
>>
>> ; RUN CONTROL PARAMETERS =
>> ; MARTINI - Most simulations are stable with dt=40 fs,
>> ; some (especially rings) require 20-30 fs.
>> ; The range of time steps used for parametrization
>> ; is 20-40 fs, using smaller time steps is therefore not recommended.
>>
>> 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 =
>>
>>
> Is this the entirety of your md.mdp file? If so, all other options will be
> set to default, and these may or may not (read: likely will not) be
> appropriate for your system. A number of factors can lead to a segmentation
> fault, but in generic terms, something became unstable. Check the output -
> look at the trajectory to see where things start to fall apart. Helpful
> messages are usually printed in the log file as well. Beyond that, please
> consult the following:
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> -Justin
>
> --
> ========================================
>
> 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
>
> ========================================
> --
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