On 3/06/2011 3:06 AM, Elisabeth wrote:
Hello all,
I am getting the error below at the very beginning of the simulation
(both serial and parallel). I am sure I did not encounter this problem
before with the same input files. This has just happened now. I really
have no clue why this is happening. could you please help me? Thank
you all in advance.
You broke the simulation. Do not use parinello-rahman for equilibration.
It's only good close to equilibrium, and can oscillate wildly under the
wrong conditions. Generate velocities on a structure whose density is
appropriate for the ensemble you're working with, equilibrate, then
compress in stages, very gently. I've lost track of the number of times
I've suggested people not just randomly apply some large pressure on
some random configuration and expect it to work.
Mark
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, 0.00000e+00, 0.00000e+00}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
; Run control
integrator = md
dt = 0.002
nsteps = 1000000 ;5000
nstcomm = 100
; Output control
nstenergy = 100
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 1000
; Neighbor searching
nstlist = 10
ns_type = grid
; Electrostatics/VdW
coulombtype = Shift
vdw-type = Shift
rcoulomb-switch = 0
rvdw-switch = 0.9 ;0
; Cut-offs
rlist = 1.25
rcoulomb = 1.0
rvdw = 1.0
; Temperature coupling
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
; Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 1
compressibility = 3.5e-5
ref_p = 10
; Velocity generation
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
; Bonds
constraints = all-bonds
constraint-algorithm = lincs
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