[gmx-users] core dumped during equilibration in gromacs

[ISHRAT JAHAN]

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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