[gmx-users] segmentation fault after mdrun

[Mark Abraham]

Nikit sharan wrote:
> Hello sir,
> 
> Thanks for your suggestion.Then as u suggested i start the work from
> scratch and did the equilibriation  again, there is nothing wrong with
> the topology also because it was taken from tiemann's website.The only
> message that it gives after equlibriation run is
> 
> "Steepest Descents converged to machine precision in 159 steps,
> but did not reach the requested Fmax < 1e-05.
> Potential Energy  = -3.3737231e+05
> Maximum force     =  2.6356035e+03 on atom 4665
> Norm of force     =  1.2290095e+04"
> 
> do i have to upgrade to double precision for simuating dppc
> bilayer?but many of them worked fine with single precision alone.

I would guess not. 1e-5 is an extremely small Fmax. Why are you using 
that value?

> When i proceded with the production run, again either its not giving
> run with 50000 steps or when i reduced step from 50000 to 50 to check
> what's the output then it gives me an error saying "
> 
> Warning: pressure scaling more than 1%, mu: 1.12479 1.12479 1.00476
> 
> Back Off! I just backed up step7018.pdb to ./#step7018.pdb.1#
> Wrote pdb files with previous and current coordinates
> Segmentation fault "
> 
> since its giving an error with pressure scaling, the parameter that i
> need to adjust is ref_p??by default i said that to 1.0?Now what value
> i have to change.

Probably this is a symptom of the problem, not the problem itself. See 
http://wiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25

> I willl be really thanful if you have a look at the segmentation fault also.

"Segmentation fault" just indicates some catastrophic failure.

> title                    = Yo
> cpp                      = cpp
> include                  =
> define                   =
> integrator               = md
> tinit                    = 0
> dt                       = 0.005

See the final line of the above link.

> nsteps                   = 50000
> init_step                = 0
> comm-mode                = Linear
> nstcomm                  = 1
> comm-grps                = system
> nstxout                  = 200
> nstvout                  = 0
> nstfout                  = 0
> nstcheckpoint            = 1000
> nstlog                   = 100
> nstenergy                = 100
> nstxtcout                = 1000
> xtc-precision            = 1000
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.0
> domain-decomposition     = no
> coulombtype              = Cut-off
> rcoulomb-switch          = 0
> rcoulomb                 = 1.0
> epsilon-r                = 1
> vdw-type                 = Cut-off
> rvdw-switch              = 0
> rvdw                     = 1.0
> DispCorr                 = EnerPres
> table-extension          = 1
> fourierspacing           = 0.12
> Pcoupl                   = berendsen
> Pcoupltype               = semiisotropic
> tau_p                    = 0.5 0.5 0.5
> compressibility          = 4.5e-5 4.5e-5 4.5e-5
> ref_p                    = 1.0 1.0 1.0
> andersen_seed            = 815131

Mark