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

[Justin A. Lemkul]

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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