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

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto: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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 

-- 
========================================

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

========================================