[gmx-users] Decane layer

[M.Naser]

Hi All,

I have a decane box with 730 kg/m^3 and trying to run trial simulation but
crashing on me. It might be due to the bad contact. Is there any way I can
avoid that?

My mdp file as follows:

title		    =  Decane
cpp                 =  /lib/cpp
;define              =  -DPOSRES ;  -DFLEX_SPC  -DFLEXIBLE
;include             =  -I/home/bio/mn2/tutor/project1/

integrator          = md
dt                  = 0.001
nsteps              = 1000000
tint		    = 0
init_step           = 0
comm_mode           = linear
nstcomm             = 1




nstlist             = 10
ns_type 	    = grid
pbc                 = xyz
rlist		    = 0.9




coulombtype	    = PME
rcoulomb-switch     = 0
rcoulomb            = 0.9
vdwtype		    = switch
rvdw-switch	    = 0.8
rvdw                = 0.9
fourierspacing     = 0.1
pme_order          = 4
ewald_rtol          =1e-5
ewald_geometry      =3dc
surface_epsilon     =0
optimize_fft        =yes
DispCorr            = no
table-extension     = 1

Tcoupl              =  Berendsen
tc_grps	            = system
tau_t               =  0.1
ref_t		    =  300

Pcoupl              = no

constraints               = all-bonds
constraint_algorithm      = shake ;lincs
unconstrained_start       = no
shake_tol                 = 0.0001


nstxout            = 1000
nstvout            = 1000
nstfout            = 0
nstlog            =  1000
nstenergy         =  1000
nstxtcout         =  1000
xtc_precision     = 1000

Thanks in advance,

Abu





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