On 12/17/12 9:14 AM, Kieu Thu Nguyen wrote:
Dear Justin,
The nvt.mdp file is:
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 = no ; first dynamics run
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 = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; 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 Non-Protein ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group,
in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
Are there any something abnormal ?
Not here. The log file should have a breakdown of the interaction ranges, which
it establishes right before the fatal error. That would be much more
informative. It could be any number of things - pair interaction, restraint in
the topology, broken starting structure, etc.
-Justin
On Mon, Dec 17, 2012 at 8:56 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 12/17/12 8:53 AM, Kieu Thu Nguyen wrote:
Dear All,
I'm practising the tutorial 2a (protein in water) in the MARTINI tutorial.
After doing step 6 (Do a short energy minimization and position restrained
simulation),i carry out running NVT equilibrium. But it appears the error
in the terminal :
Fatal error:
There is no domain decomposition for 2 nodes that is compatible with the
given box and a minimum cell size of 5.2375 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS
settings
Look in the log file for details on the domain decomposition
What can i do to fix this error ?
http://www.gromacs.org/**Documentation/Errors#There_is_**
no_domain_decomposition_for_n_**nodes_that_is_compatible_with_**
the_given_box_and_a_minimum_**cell_size_of_x_nm<http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm>
The fact that the minimum size is over 5 nm is very odd. Are there very
long-range bonded interactions of some sort? Normally the minimum box size
is very close to the value of the longest cutoff unless something abnormal
is present.
-Justin
--
==============================**==========
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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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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