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

[Justin Lemkul]

On 2/5/14, 10:58 AM, Steven Neumann wrote:
> Thank you. Can you specify what does long mean? Is there any limit?
>

You can define whatever interactions you want, but the size of each DD cell will 
be assigned based on that interaction.  As the previous error message indicated, 
the minimum DD cell size you can partition your system into is on the order of 
10 nm.  If the system size is not compatible with such partitioning, you can't 
use DD.

-Justin

>
> On Wed, Feb 5, 2014 at 3:49 PM, Justin Lemkul <jalemkul at vt.edu
> <mailto: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
>     <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
>     <tel:%28410%29%20706-7441>
>     http://mackerell.umaryland.__edu/~jalemkul
>     <http://mackerell.umaryland.edu/~jalemkul>
>
>     ==============================__====================
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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

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