[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
Sonia Aguilera
sm.aguilera37 at uniandes.edu.co
Tue Feb 12 23:24:47 CET 2013
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?
Thank you in advance
Sonia Aguilera
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