[gmx-users] segmentation fault after mdrun

[Nikit sharan]

Hello sir,

Thanks for your suggestion.Then as u suggested i start the work from
scratch and did the equilibriation  again, there is nothing wrong with
the topology also because it was taken from tiemann's website.The only
message that it gives after equlibriation run is

"Steepest Descents converged to machine precision in 159 steps,
but did not reach the requested Fmax < 1e-05.
Potential Energy  = -3.3737231e+05
Maximum force     =  2.6356035e+03 on atom 4665
Norm of force     =  1.2290095e+04"

do i have to upgrade to double precision for simuating dppc
bilayer?but many of them worked fine with single precision alone.


When i proceded with the production run, again either its not giving
run with 50000 steps or when i reduced step from 50000 to 50 to check
what's the output then it gives me an error saying "

Warning: pressure scaling more than 1%, mu: 1.12479 1.12479 1.00476

Back Off! I just backed up step7018.pdb to ./#step7018.pdb.1#
Wrote pdb files with previous and current coordinates
Segmentation fault "

since its giving an error with pressure scaling, the parameter that i
need to adjust is ref_p??by default i said that to 1.0?Now what value
i have to change.


I willl be really thanful if you have a look at the segmentation fault also.

title                    = Yo
cpp                      = cpp
include                  =
define                   =
integrator               = md
tinit                    = 0
dt                       = 0.005
nsteps                   = 50000
init_step                = 0
comm-mode                = Linear
nstcomm                  = 1
comm-grps                = system
nstxout                  = 200
nstvout                  = 0
nstfout                  = 0
nstcheckpoint            = 1000
nstlog                   = 100
nstenergy                = 100
nstxtcout                = 1000
xtc-precision            = 1000
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.0
domain-decomposition     = no
coulombtype              = Cut-off
rcoulomb-switch          = 0
rcoulomb                 = 1.0
epsilon-r                = 1
vdw-type                 = Cut-off
rvdw-switch              = 0
rvdw                     = 1.0
DispCorr                 = EnerPres
table-extension          = 1
fourierspacing           = 0.12
Pcoupl                   = berendsen
Pcoupltype               = semiisotropic
tau_p                    = 0.5 0.5 0.5
compressibility          = 4.5e-5 4.5e-5 4.5e-5
ref_p                    = 1.0 1.0 1.0
andersen_seed            = 815131