[gmx-users] Simulation problem

[Justin Lemkul]

On 2/25/13 1:01 AM, Jernej Zidar wrote:
> Hi.
>    I've been running some polymer simulations on our cluster and I'm
> getting this error:
> One of the box vectors has become shorter than twice the cut-off
> length or box_yy-|box_zy| or box_zz has become smaller than the
> cut-off.
>
>    What does this error mean? I imagine it is somehow related to the
> unit cell. Could the error be related to the fact that the unit cell
> is rather long (along x axis) but short along the other axis. The
> thickness of the solvation layer is 2.0 nm, which should be OK.
>

The error means that fluctuation of the unit cell dimensions will cause 
violation of the minimum image convention.  Either the simulation box has become 
unstable and is going to crash, or you have larger fluctuations than you 
anticipated in the pressure (and thus box size) when building the system.

-Justin

>    I use the following input:
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 25000000      ; 2 * 25000000 = 50 ns
> dt              = 0.002         ; 2 fs
>
> ; Bond parameters
> continuation            =       yes     ; Restarting after NVT
> constraint_algorithm    =       lincs   ; holonomic constraints
> constraints             =       hbonds  ; all bonds (even heavy atom-H
> bonds) constrained
> lincs_iter              =       1       ; accuracy of LINCS
> lincs_order             =       4       ; also related to accuracy
>
> ; Output control
> nstxout         = 10000         ; save coordinates every 20 ps
> nstenergy       = 1000          ; save energies every 20 ps
> nstlog          = 1000          ; update log file every 20 ps
>
> ; Neighbour searching
> ns_type         = grid
> nstlist         = 5
> rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
>
> ; Non-bonded interactions
> vdw-type        = shift
> rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
> rvdw-switch     = 0.8
>
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.12          ; grid spacing for FFT
> optimize-fft    = yes           ; optimize the FFT transforms for the
> current problem
>
> ; Temperature coupling is on for three groups
> tcoupl          = Nose-Hoover           ; More accurate thermostat
> tc-grps         = POLYMER Water_CL_NA   ; three coupling groups - more accurate
> tau_t           = 0.5   0.5             ; time constant, in ps
> ref_t           = 300   300             ; reference temperature, one
> for each group, in K
>
> ; Pressure coupling is on
> pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
> pcoupltype      = isotropic             ; uniform scaling of x-y box
> vectors, independent z
> tau_p           = 5.0                   ; time constant, in ps
> ref_p           = 1.0                   ; reference pressure, x-y, z (in bar)
> compressibility = 4.5e-5                ; isothermal compressibility, bar^-1
>
> ; Miscelanous
> gen_vel         = no    ; Velocity generation is off
> dispcorr        = no    ; account for cut-off vdW scheme
>
> ; Center of mass (COM) motion removal
> ; Reason: these options remove motion of the protein/bilayer relative
> to the solvent/ions
> nstcomm         = 10
> comm-mode       = Linear
> comm-grps       = POLYMER Water_CL_NA
>
> - - -
>
> Thanks in advance for any help or advice,
> Jernej Zidar
>

-- 
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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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