[gmx-users] error: Only triclinic boxes...
Elisabeth
katesedate at gmail.com
Thu Jun 2 21:13:52 CEST 2011
Dear Justin,
I find:
box (3x3):
box[ 0]={ 1.60000e+01, 0.00000e+00, 0.00000e+00}
box[ 1]={ 0.00000e+00, 1.60000e+01, 0.00000e+00}
box[ 2]={ 0.00000e+00, 0.00000e+00, 1.60000e+01}
box_rel (3x3):
box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
box_rel[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
boxv (3x3):
boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
pres_prev (3x3):
pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
svir_prev (3x3):
svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
fvir_prev (3x3):
fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
nosehoover_xi: not available
x (2896x3):
x[ 0]={-7.49400e+00, 4.57000e-01, 5.00000e-01}
x[ 1]={-7.58200e+00, 5.21000e-01, 5.00000e-01}
x[ 2]={-7.49600e+00, 3.94000e-01, 4.11000e-01}
x[ 3]={-7.49600e+00, 3.94000e-01, 5.89000e-01}
x[ 4]={-7.36800e+00, 5.43000e-01, 5.00000e-01}
x[ 5]={-7.36800e+00, 6.06000e-01, 5.89000e-01}
x[ 6]={-7.36800e+00, 6.06000e-01, 4.11000e-01}
x[ 7]={-7.24200e+00, 4.57000e-01, 5.00000e-01}
x[ 8]={-7.24200e+00, 3.94000e-01, 4.11000e-01}
x[ 9]={-7.24200e+00, 3.94000e-01, 5.89000e-01}
x[ 10]={-7.11700e+00, 5.43000e-01, 5.00000e-01}
x[ 11]={-7.11700e+00, 6.06000e-01, 5.89000e-01}
x[ 12]={-7.11700e+00, 6.06000e-01, 4.11000e-01}
x[ 13]={-6.99100e+00, 4.57000e-01, 5.00000e-01}
I made box bigger to remove bad contacts in initial configuration (although
I have been using the same gro file before and never got such error). Do you
recommend I reinstall 4.5.4 ?
Appreciate any help...
Regards,
On 2 June 2011 14:47, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
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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
>
> ========================================
> --
> gmx-users mailing list 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!
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