Elisabeth wrote:
Hello Justin,
Thank you. I am using
gmxdump -s *.tpr -om to produce mdout.mdp file but I dont see box
You don't need an mdout.mdp file, nor would box vectors be present in one. What
you're looking for is the box information present in the .tpr file. Run:
gmxdump -s topol.tpr > out
Then search in the "out" file for the box information.
vector information. This error happens at the very beginning. I see no
steps are calculated.
Then the input box information is likely corrupt, or the simulation blows up at
the very start of the simulation (i.e. step 0).
-Justin
On 2 June 2011 13:11, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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.
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.
Your system is probably blowing up. "Nan" means "not a number," so
the box vectors have become either infinitely large or small.
Either the input coordinate file contained a malformed or
non-existent box, or the simulation is collapsing along the way
somewhere. Does the simulation run for a while before printing
this, or is it right away?
You can check the starting box vectors in the .tpr file with gmxdump
to verify that they are sensible.
-Justin
; 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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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