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

[Steven Neumann]

Thanks a lot!

Steven


On Wed, Feb 5, 2014 at 4:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/5/14, 11:05 AM, Steven Neumann wrote:
>
>> Maybe you know how do they keep nanotubes rigid then?
>>
>>
> Nope, sorry.
>
> -Justin
>
>
>> On Wed, Feb 5, 2014 at 3:58 PM, Steven Neumann <s.neumann08 at gmail.com
>> <mailto:s.neumann08 at gmail.com>> wrote:
>>
>>     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
>>     <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
>
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