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

[Elisabeth]

On 3 June 2011 03:25, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> On 3/06/2011 3:06 AM, 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.
>>
>
> You broke the simulation. Do not use parinello-rahman for equilibration.
> It's only good close to equilibrium, and can oscillate wildly under the
> wrong conditions. Generate velocities on a structure whose density is
> appropriate for the ensemble you're working with, equilibrate, then compress
> in stages, very gently. I've lost track of the number of times I've
> suggested people not just randomly apply some large pressure on some random
> configuration and expect it to work.
>


Dear gmx experts,

The reason I was getting error below

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.

was that I had mistakenly decreased box size to a size considerably smaller
than initial structure. One of my colleagues provided me with input files to
get an idea how these runs work and we were surprised how come the
simulation that would run before I receive it, is giving error message
above. I checked on gro file several times as you suggested but did not
notice the last line..!

Thanks Mark, Justin and Dr. Chaban for your comments.

Best,

>
>
>
>
>
>>
>> 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.
>>
>>
>>
>> ;        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
>>
>>
>>
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