[gmx-users] Error with LINC warning

[vivek sharma]

Hi there,

I am running gromacs in parellel with mpi interface..(np 20)
but it is exiting with the following error in output file
.
.
.
.Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 1.151530 (between atoms 2685 and 2686) rms 0.187095
bonds that rotated more than 30 degrees:
.
.
.
.
Wrote pdb files with previous and current coordinates
srun: error: n26: task3: Segmentation fault
srun: Terminating job

I am not understanding the error, Can anybody help me in understanding that
what does this error indicates ?
following is the md.mdp file I am using to run simulation. Is there any
problem with the parameters ?

md.mdp..............................................
title               = trp_drg MD
cpp                 = /lib/cpp ; location of cpp on SGI
constraints         = all-bonds
integrator          = md
dt                  = 0.02 ; ps !
nsteps              = 250000 ; total 5000 ps.
nstcomm             = 1
nstxout             = 25000 ; output coordinates every 500.0 ps
nstvout             = 0
nstfout             = 0
nstlist             = 5
ns_type             = grid
rlist               = 0.9
coulombtype         = PME
rcoulomb            = 0.9
rvdw                = 1.4
fourierspacing      = 0.12
fourier_nx        = 0
fourier_ny        = 0
fourier_nz        = 0
pme_order         = 6
ewald_rtol        = 1e-5
optimize_fft      = yes
; Berendsen temperature coupling is on in four groups
Tcoupl                = berendsen
tau_t                 = 0.1         0.1   0.1
tc-grps               = protein     NDP   sol
ref_t                 = 300         300   300
; Pressure coupling is on
Pcoupl              = berendsen
pcoupltype          = isotropic
tau_p               = 0.5
compressibility     = 4.5e-5
ref_p               = 1.0
; Generate velocites is on at 300 K.
gen_vel             = yes
gen_temp            = 300.0
gen_seed            = 173529

Any suggestion would be of great help..

With Thanks,
Vivek
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