[gmx-users] error when running NVT equilibrium

[Justin Lemkul]

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 <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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-- 
========================================

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

========================================