[gmx-users] segmentation fault after mdrun
Mark.Abraham at anu.edu.au
Sat Feb 21 11:37:41 CET 2009
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
> 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
> 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
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