[gmx-users] error when running NVT equilibrium

[Kieu Thu Nguyen]

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 ?


On Mon, Dec 17, 2012 at 8:56 PM, Justin Lemkul <jalemkul at 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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