[gmx-users] simulation of long chains in vacuum

[Rongliang Wu]

Hello, gmx-users，
	i generated a chain of 1000 units and intended to simulate in vacuum, but the system exploded and the mdp file is as follows:

title                    = PE
cpp                      = /usr/bin/cpp
include                  = 
define                   = 
integrator               = md
dt                       = 0.002
nsteps                   = 100000
nstxout                  = 5000
nstvout                  = 5000
nstlog                   = 5000
nstenergy                = 500
nstxtcout                = 2000
xtc_grps                 =
energygrps               =
comm_mode		 = angular
nstlist                  = 0
ns_type                  = simple
rlist                    = 0
rvdw                     = 0
rcoulomb		 = 0
pbc			 = no
tcoupl                   = Berendsen
tc-grps                  = system
tau_t                    = 0.1 
ref_t                    = 300 
Pcoupl                   = no
;Pcoupltype               = isotropic
;tau_p                    = 1.0
;compressibility          = 4.5e-4
;ref_p                    = 1.0 
;annealing								 = single
;annealing_npoints				 = 15
;annealing_time					 = 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70
;annealing_temp					 = 370 365 360 355 350 345 340 335 330 325 320 315 310 305 300
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
constraints              = all-bonds
optimize_fft		 = yes

are there any obvious errors? 
and my system is quite large, about   49.90900  70.12100 231.85800 ns
is there any upper limits for gromacs systems?

Regards

Thanks
 				

　　　　　　　　Rongliang Wu
　　　　　　　　wurl04 at iccas.ac.cn
　　　　　　　　　　2006-05-10