[gmx-users] core dumped during equilibration in gromacs

[Mark Abraham]

Hi,

Like that page says, what happens when you simulate your solvent box alone?
And your protein in vacuum? Or choose a smaller PR time step? You have a
problem with a complex system, so simplify things in order to find your
problem.

Mark

On Wed, Mar 22, 2017 at 12:30 PM ISHRAT JAHAN <jishrat17 at gmail.com> wrote:

> Firstly I prepared urea box using amber99sb-ildn ff ,then do pdb2gmx of
> protein using amber99sb-ildn force field ,then do editconf with -d=1.46,
> genbox with -cs =urea_box generated previously and then energy minimization
> and then equilibration, segmentation fault occured at end. Please help me
> in solving this problem.
> Here is my em.mdp and pr.mdp file-
> em.mdp
> ;^M
> ;       User spoel (236)^M
> ;       Wed Nov  3 17:12:44 1993^M
> ;       Input file^M
> ;^M
> cpp                 =  /usr/bin/cpp^M
> define              =  -DFLEX_SPC^M
> constraints         =  all-bonds
> integrator          =  steep ^M
> nsteps              =  50000
> ;       Energy minimizing stuff^M
> emtol               =  1000^M
> emstep              =  0.01^M
> nstlist             =  1^M
> nstcomm             =  100^M
> ns_type             =  grid^M
> rlist               =  0.8 ^M
> coulombtype         =  PME^M
> rcoulomb            =  0.8^M
> rvdw                =  0.8
> pbc                 =  xyz
> fourierspacing = 0.12^M
> fourier_nx = 0^M
> fourier_ny = 0^M
> fourier_nz = 0^M
> pme_order = 4^M
> ewald_rtol = 1e-5^M
> optimize_fft = yes^M
> Tcoupl              =  no^M
> Pcoupl              =  no^M
> gen_vel             =  no^M
> ~
>
> PR_nvt.mdp
> ;^M
> ;       User spoel (236)^M
> ;       Wed Nov  3 17:12:44 1993^M
> ;       Input file^M
> ;^M
> title               =  Yo^M
> cpp                 =  /usr/bin/cpp^M
> define              =  -DPOSRES^M
> constraints         =  all-bonds^M
> constraintalgorithm =  LINCS^M
> integrator          =  md^M
> dt                  =  0.002    ; ps !^M
> nsteps              =  50000    ; total 10 ps.^M
> nstcomm             =  1000^M
> nstxout             =  1000^M
> nstvout             =  1000^M
> nstfout             =  0^M
> nstlog              =  10^M
> nstenergy           =  10^M
> nstlist             =  10^M
> ns_type             =  grid^M
> rlist               =  1.4
> coulombtype         =  PME^M
> rcoulomb            =  1.4
> rvdw                =  1.4
> fourierspacing = 0.12^M
> fourier_nx = 0^M
> fourier_ny = 0^M
> fourier_nz = 0^M
> pme_order = 4^M
> ewald_rtol = 1e-5^M
> optimize_fft = yes^M
> ; Berendsen temperature coupling is on in two groups^M
> Tcoupl              =  V-rescale^M
> tc-grps             =  System    ^M
> tau_t               =  0.1       ^M
> ref_t               =  300  ^M
> ; Energy monitoring^M
> energygrps          =  System^M
> ; Pressure coupling is off^M
>
>
> On Wed, Mar 22, 2017 at 4:11 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > All of the advice there still applies to trying to move from a successful
> > energy minimization to a dynamical simulation. Without knowing all the
> > details of how you prepared everything, that advice is all anybody can
> say.
> >
> > Mark
> >
> > >
> > > On Wed, Mar 22, 2017 at 11:08 AM ISHRAT JAHAN <jishrat17 at gmail.com>
> > wrote:
> > >
> > > I have reduced the force and  timestep as given at
> > http://www.gromacs.org/
> > > Documentation/Terminology/Blowing_Up
> > > <http://www.gromacs.org/Documentation/Terminology/Blowing_Up>
> > > <http://www.gromacs.org/Documentation/Terminology/Blowing_Up>  but
> still
> > > getting an error like-
> > > Double precision normally gives you higher accuracy.
> > > You might need to increase your constraint accuracy, or turn
> > > off constraints alltogether (set constraints = none in mdp file)
> > >
> > > writing lowest energy coordinates.
> > >
> > > Back Off! I just backed up prion_em.gro to ./#prion_em.gro.1#
> > >
> > > Steepest Descents converged to machine precision in 726 steps,
> > > but did not reach the requested Fmax < 1000.
> > > Potential Energy  = -1.7322245e+05
> > > Maximum force     =  8.0706294e+03 on atom 2216
> > > Norm of force     =  1.4435008e+02
> > >
> > > if i proceed for pr with this result segmentation fault occured again.
> > >
> > >
> > --
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