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

[mtso]

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:


 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.  



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