[gmx-users] step 0Segmentation fault: 11

[Mark Abraham]

Huge forces lead to crazy displacements whose next forces are looked up
outside the boundaries of your table, which leads to a segmentation fault.
GROMACS doesn't waste its time checking for this,  since that would hurt
everyone's performance and gain only a descriptive error that something is
horribly broken!

Mark
On Nov 28, 2013 1:36 AM, "Valentina" <valentina.erastova at durham.ac.uk>
wrote:

> I still cannot resolve this problem. Is there any way to find out what is
> causing Segmentation Fault? Normally Gromacs provides quite comprehendible
> errors, but this one.
>
> I have checked the charges against DFT.
>
> I also have the output of the system simulated with Discover. I am using
> that force field (obviously tabulated) and charges used there.
>
> The initial model is taken from Xray and optimised with DFT.
>
> Still md.log terminates with unrealistic T & P on 0th step:
>
>      /      Step           Time         Lambda
>               0        0.00000        0.00000
>
>
> Grid: 4 x 3 x 3 cells
>    Energies (kJ/mol)
>      Tab. Bonds    Tab. Angles        LJ (SR)   Coulomb (SR)      Potential
>     5.44943e+06    4.41001e+11    9.86202e+02   -2.42548e+05    4.41006e+11
>     Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
>     1.97584e+16    1.97588e+16    1.97588e+16    2.24716e+15    1.99874e+16
> /
>
>
> BTW - I noticed that I get continuously get a 0 dimension in z direction if
> I do energy minimisation with plc = xy - is that right?
>
> My equil.mdp is following - may be some problem there?
> I do energy minimisation before equilibration.
>
> /integrator               = md
> nsteps                   = 100
> dt                       = 0.001
> ;comm_mode = ANGULAR
> nstenergy                = 1
> nstxout                  = 1
> nstvout                  = 1
> energygrps               = System
> ; cut-offs at 1nm
> rlist                    = 0.8
> nstlist                  = 10
> coulombtype              = user
> rcoulomb                 = 0.8
> vdw-type                 = user
> rvdw                     = 0.8
> pbc                      = xyz
> periodic_molecules       = yes
> ; set temperature to 300K
> tcoupl                   = V-rescale
> tc-grps                  = System
> tau-t                    = 1.0
> ref-t                    = 500
> ; and pressure to 1 bar
> pcoupl          = no
> compressibility  =  4.5e-5
> ; generate initial velocities
> gen-vel                  = no/
>
> I am running with 6-9 LJ, that I provide input to mdrun
>
>
>
>
> I do energy minimisation before equilibration.
> em.mdp is
> /integrator               = steep
> nsteps                   = 500000
> emtol                    = 1
> emstep                   = 0.001
> nstxout                  = 1
> nstenergy                = 1
> rlist                    = 0.8
> pbc                      = xyz
> periodic_molecules       = yes
> coulombtype              = user
> rcoulomb                 = 0.8
> vdw-type                 = user
> rvdw                     = 0.8
> constraints             = none/
>
>
> I get following output:
>
> /Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+00
>    Number of steps    =       500000
> Step=    2, Dmax= 5.0e-04 nm, Epot=  4.40635e+11 Fmax= 8.77355e+10, atom=
> 223
> Step=    4, Dmax= 3.0e-04 nm, Epot=  4.40403e+11 Fmax= 9.61163e+10, atom=
> 263
> Step=    6, Dmax= 1.8e-04 nm, Epot=  4.40248e+11 Fmax= 1.01812e+11, atom=
> 833
> Step=    8, Dmax= 1.1e-04 nm, Epot=  4.40181e+11 Fmax= 9.36260e+10, atom=
> 83
> Step=   10, Dmax= 6.5e-05 nm, Epot=  4.40142e+11 Fmax= 9.89456e+10, atom=
> 833
> Step=   12, Dmax= 3.9e-05 nm, Epot=  4.40115e+11 Fmax= 8.24990e+10, atom=
> 105
> Step=   14, Dmax= 2.3e-05 nm, Epot=  4.40094e+11 Fmax= 4.88140e+10, atom=
> 105
> Step=   19, Dmax= 1.7e-06 nm, Epot=  4.40098e+11 Fmax= 4.47573e+10, atom=
> 223
> Energy minimization has stopped, but the forces havenot converged to the
> requested precision Fmax < 1 (whichmay not be possible for your system). It
> stoppedbecause the algorithm tried to make a new step whose sizewas too
> small, or there was no change in the energy sincelast step. Either way, we
> regard the minimization asconverged to within the available machine
> precision,given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, butthis is often not
> needed for preparing to run moleculardynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up confout.gro to ./#confout.gro.4#
>
> Steepest Descents converged to machine precision in 20 steps,
> but did not reach the requested Fmax < 1.
> Potential Energy  =  4.4009390e+11
> Maximum force     =  4.8813974e+10 on atom 105
> Norm of force     =  5.4008571e+09
> /
>
> I cannot recollect how energy minimisation output should look like - is
> this
> right?
>
>
> It would be great to hear some suggestions how to pin-point the problem.
>
> Thank you for your help
>
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/step-0Segmentation-fault-11-tp5012832p5012866.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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