[gmx-users] error: Only triclinic boxes...

[Elisabeth]

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 <jalemkul at 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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