[gmx-users] Error in npt run - box size/ triclinic skew factor

[Justin Lemkul]

On 10/30/12 4:23 PM, mtso wrote:
> When trying to do an npt run, I get the fatal error: The X-size of the box
> (3.999511) times the triclinic skew factor (1.000000) is smaller than the
> number of DD cells (4) times the smallest allowed cell size (1.000000).  I
> should mention, I'm brand new to using gromacs so any assistance is greatly
> appreciated.  My nvt run was fine.  I used the following mdp file:
>

The error means your system has become unstable and is about to blow up.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Are you running the tutorial?  The .mdp file would indicate you are, but the 
system is very robust and I have not seen this happen.

-Justin

>
>   title		= OPLS Lysozyme NPT equilibration
> define		= -DPOSRES	; position restrain the protein
> ; Run parameters
> integrator	= md		; leap-frog integrator
> nsteps		= 50000		; 2 * 50000 = 100 ps
> dt		= 0.002		; 2 fs
> ; Output control
> nstxout		= 100		; save coordinates every 0.2 ps
> nstvout		= 100		; save velocities every 0.2 ps
> nstenergy	= 100		; save energies every 0.2 ps
> nstlog		= 100		; update log file every 0.2 ps
> ; Bond parameters
> continuation	= yes		; Restarting after NVT
> constraint_algorithm = lincs	; holonomic constraints
> constraints	= all-bonds	; all bonds (even heavy atom-H bonds) constrained
> lincs_iter	= 1		; accuracy of LINCS
> lincs_order	= 4		; also related to accuracy
> ; Neighborsearching
> ns_type		= grid		; search neighboring grid cells
> nstlist		= 5		; 10 fs
> rlist		= 1.0		; short-range neighborlist cutoff (in nm)
> rcoulomb	= 1.0		; short-range electrostatic cutoff (in nm)
> rvdw		= 1.0		; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype	= PME		; Particle Mesh Ewald for long-range electrostatics
> pme_order	= 4		; cubic interpolation
> fourierspacing	= 0.16		; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl		= V-rescale	; modified Berendsen thermostat
> tc-grps		= Protein ; two coupling groups - more accurate
> tau_t		= 0.1	; time constant, in ps
> ref_t		= 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 box vectors
> tau_p		= 2.0		; time constant, in ps
> ref_p		= 1.0		; reference pressure, in bar
> refcoord_scaling	= com	; scale center of mass of reference coordinates
> compressibility = 4.5e-5	; isothermal compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc		= xyz		; 3-D PBC
> ; Dispersion correction
> DispCorr	= EnerPres	; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel		= no		; Velocity generation is off
>
> Thanks in advance.
>
>
>
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-npt-run-box-size-triclinic-skew-factor-tp5002482.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

-- 
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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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