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

[Mark Abraham]

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.

Mark

>
>
> 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
>
>