Hello Justin,
Thank you. I am using
gmxdump -s *.tpr -om to produce mdout.mdp file but I dont see box vector
information. This error happens at the very beginning. I see no steps are
calculated.
On 2 June 2011 13:11, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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