[gmx-users] core dumped during equilibration in gromacs
Mark Abraham
mark.j.abraham at gmail.com
Wed Mar 22 12:48:56 CET 2017
Hi,
Thus you can suspect the problem is that there's some issue with the
combination of the two structures that can't be resolved by a small time
step because the forces are extremely large. That suggests you have some
extreme atomic clash, which you can investigate by visualizing the solvated
structure. Look also at what genbox told you about what it thought about
VDW radii while it was doing its job, or use whatever options it has to
choose larger ones.
Mark
On Wed, Mar 22, 2017 at 12:40 PM ISHRAT JAHAN <jishrat17 at gmail.com> wrote:
> 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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