[gmx-users] core dumped during equilibration in gromacs
ISHRAT JAHAN
jishrat17 at gmail.com
Wed Mar 22 12:40:24 CET 2017
it run smoothly when solvent box and protein is simulated alone.
Problem arises when i try to simulate both. I have also reduced the pr time
step still error occur.
On Wed, Mar 22, 2017 at 5:04 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> 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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