[gmx-users] There is no domain decomposition for nodes that is compatible

[Steven Neumann]

Thank you. Can you specify what does long mean? Is there any limit?


On Wed, Feb 5, 2014 at 3:49 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/5/14, 10:46 AM, Steven Neumann wrote:
>
>> Can you please advise? With large constraints it does not work... with [
>> distance_restraints ] it works but only with mdrun -nt 1
>> my mdp:
>>
>> disre                =  simple
>> disre-fc             =  1000
>>
>> integrator               = md
>> tinit                    = 0.0
>> dt                       = 0.008
>> nsteps                   = 100000      ; 500 ns
>> nstcomm                  = 100
>> nstcalcenergy         = 100
>>
>> nstxout             = 0
>> nstvout               = 0
>> nstenergy            = 0
>> nstlog                   = 100
>> nstxtcout                = 100
>>
>> freezegrps         = System
>> freezedim          = N N Y
>> energygrps               = ACI BAS GLY NON POL
>> energygrp_table          = ACI ACI ACI BAS ACI GLY ACI NON ACI POL BAS BAS
>> BAS GLY GLY GLY GLY NON GLY POL NON BAS NON NON POL BAS POL NON POL POL
>> table-extension         = 1.0
>>
>>
>> nstlist                  = 10
>> ns_type                  = grid
>> pbc                      = xyz
>> rlist                    = 2.0
>>
>>
>> coulombtype          = User
>> rcoulomb                 = 2.0
>>
>> vdw_type                 = User
>> rvdw                     = 2.0
>>
>>
>> tcoupl               = V-rescale
>> tc_grps               = System
>> tau_t                 = 0.1
>> ref_t                 = 300
>> pcoupl             = no
>>
>> gen_vel                  = yes
>> gen_temp                 = 300
>> gen_seed                 = -1
>>
>>
>> constraints              = none
>> constraint_algorithm     = Lincs
>> continuation             = no
>> lincs_iter              = 1
>> lincs_order              = 4
>>
>>
>>
>>
>>
>> I will really appreciate.
>>
>>
> DD cells are set up based on bonded geometry and a host of other factors.
>  Any very long bond or restraint will seriously inhibit the ability of DD
> to function.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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