[gmx-users] shake and lincs crashing

[Bamidele Adisa]

Hi,
i'm running an md simulation of a phenylacetylene oligomer in water. the 
phenylacetylene has butyl sidegroups.
after minimizations using sd, cg and l-bfgs, i run a 50ps NVT simulation 
without constraints using a 0.1fs timestep.
i then try to run a 1ns NVT simulation using 1fs timestep and constraining 
all-bonds using shake and the simulation crashes after about 5-10ps.
this also happens when i use lincs. i have pasted my mdp file below.
could anyone suggest what the problem is and any solutions?
i'm using oplsaa forcefield with flexible spc water model.
thanks

integrator               = md
tinit                        = 0 ; ps
dt                           = 0.001 ; ps
nsteps                      = 1000000 ; total 1000ps
comm_mode             = Linear
nstcomm                  = 1
nstxout                    = 5000
nstvout                    = 5000
nstfout                   = 0
nstlog                     = 2000
nstenergy               = 2000
nstlist                     = 5
ns_type                  = grid
pbc                        = full
rlist                       = 1.0 ;nm
coulombtype          = cut-off
rcoulomb               = 1.4 ;nm
rcoulomb_switch   = 0.9 ;nm
epsilon_r               = 1
vdwtype                = cut-off
rvdw                     = 1.4 ;nm
rvdw_switch         = 0.9 ;nm
tcoupl                   = berendsen
tc-grps                  = PPE          SOL
tau_t                    = 0.1          0.1     ;ps
ref_t                    = 300          300     ;K
;Pcoupl                   = no
gen_vel                  = yes
gen_temp                 = 300 ;K
gen_seed                 = 173529
constraints              = all-bonds
constraint_algorithm     = shake
shake_tol                = 0.0001
unconstrained_start      = yes


______________________
Bamidele Adisa
Dept of Chemical Engineering
Clemson University
Clemson, SC 29634-0909
864-654-0586
______________________