[gmx-users] semiisotropic pressure coupling error

[Justin Lemkul]

On 6/7/18 5:59 AM, Oguz Gurbulak wrote:
> Dear Gromacs Users,
>
> When I used semiisotropic pressure coupling, I got this error message
>
> "Fatal error:
> The Y-size of the box (4.200315) times the triclinic skew factor (1.000000)
> is smaller than the number of DD cells (3) times the smallest allowed cell
> size (1.400000)"
>
>
> Could you please help me to solve this error ?

Your system has become unstable. See 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

>
> Kind regards.
>
>
> **** MDP FILE ****
>
> ; Run parameters
> integrator    = md        ; leap-frog integrator
> nsteps        = 5000000    ;
> dt            = 0.002        ;
>
> ; Output control
> nstxout        = 2000        ;
> nstvout        = 2000        ;
> nstenergy    = 2000        ;
> nstlog        = 2000        ;
>
> ; Bond parameters
> constraint_algorithm   = lincs        ;
> constraints           = all-bonds  ;
> lincs_iter           = 1     ;
> lincs_order           = 4       ;
>
>
> ; Neighbor searching
> cutoff-scheme   = Verlet
> rlist            = 1.4       ;
> ns_type        = grid
> nstlist        = 10        ;
> nstcomm         = 100
>
> ; Electrostatics
> coulombtype        = PME    ;
> rcoulomb        = 1.4    ;
> pme_order           = 4
> fourierspacing      = 0.16
> ewald-rtol          = 1e-5
>
> ; Dispersion correction
> DispCorr    = EnerPres      ;
>
>
> ; Van der Waals
> vdwtype = cutoff
> rvdw = 1.4    ;
>
>
> ; Temperature coupling is on
> tcoupl        = V-rescale            ;
> tc-grps        = ABC SOL            ;
> tau_t        = 0.1    0.1                ;
> ref_t        = 302.7 302.7                ;
>
>
> ; Pressure coupling is on
> pcoupl        = berendsen        ; Pressure coupling on in NPT
> pcoupltype    = semiisotropic            ;
> tau_p        = 2.0                    ;
> ref_p        = 50.0    1.0                ;
> compressibility = 4.5e-5    4.5e-5    ;
>
>
> ; Periodic boundary conditions
> pbc        = xyz            ; 3-D PBC
>
>
> ; Velocity generation
> continuation    = no        ;
> gen_vel        = yes        ;
> gen_temp    = 302.7        ;
> gen_seed    =  -1        ;

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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