[gmx-users] Error: The Y-size of the box times the triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size

[Justin Lemkul]

On 2/12/13 5:24 PM, Sonia Aguilera wrote:
> Hi,
>
> I was performing a NPT calculation, and I got this error:
>
> The Y-size of the box (6.002812) times the triclinic skew factor (1.000000)
> is smaller than the number of DD cells (6) times the smallest allowed cell
> size (1.000605)
>
> I also tried to change the number of processors but I got the same error. My
> system is a protein in vacuo. This is my mdp file (Taken from Justin
> Lemkul's tutorial for FE calculations:
>
> title                    = NPT equilibration
> ; Run control
> integrator               = sd       ; Langevin dynamics
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 200000    ; 444400 ps
> nstcomm                  = 100
> ;Langevin dynamics
> ld_seed                  = -1
> ; Output control
> nstxout                  = 1000
> nstvout                  = 1000
> nstfout                  = 0
> nstlog                   = 1000
> nstenergy                = 1000
> nstxtcout                = 0
> xtc-precision            = 1000
> ; Neighborsearching and short-range nonbonded interactions
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.5
> ; Electrostatics
> coulombtype              = PME
> rcoulomb                 = 1.5
> ; van der Waals
> vdw-type                 = switch
> rvdw-switch              = 0.8
> rvdw                     = 0.9
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr                  = EnerPres
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing           = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order                = 6
> ewald_rtol               = 1e-06
> epsilon_surface          = 0
> optimize_fft             = no
> ; Temperature coupling
> ; tcoupl is implicitly handled by the sd integrator
> tc_grps                  = system
> tau_t                    = 1.0
> ref_t                    = 300
> ; Pressure coupling is on for NPT
> Pcoupl                   = Parrinello-Rahman
> tau_p                    = 0.5
> compressibility          = 4.5e-05
> ref_p                    = 1.0
> ; Do not generate velocities
> gen_vel                  = no
> ; options for bonds
> constraints              = h-bonds  ; we only have C-H bonds here
> ; Type of constraint algorithm
> constraint-algorithm     = lincs
> ; Constrain the starting configuration
> ; since we are continuing from NVT
> continuation             = yes
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order              = 12
>
>
> Can you please tell my what is wrong? I runned previous nvt, npt and md
> simulation with the same box size and protein but in water. Is there any way
> of solving this problem without affecting the accuracy of the simulation?
>

NPT doesn't make sense in vacuo.  The unit cell compresses around the protein, 
leaving you with periodicity artifacts and a quasi-crystalline environment.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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