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

[Justin Lemkul]

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

-- 
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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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