[gmx-users] rlist for implicit water

[Urszula Uciechowska]

Dear Justin,

How could I change the cut-offs  to make the MD more faster in my case?

/Urszula
>
>
> On 6/3/14, 4:15 AM, Urszula Uciechowska wrote:
>> Dear Gromacs users,
>>
>> I would like to run simulations with implicit water. My protein system
>> is
>> quite big it contains 784AA. I prepared eM.mdp file (see below) however
>> I
>> am not sure if its ok especially the rlist what should I use there in
>> case
>> of such big system.
>>
>> define                  = -DFLEXIBLE
>> constraints             = none
>> integrator              = steep         ; steepest descents energy
>> minimization
>> dt                      = 0.001         ; ps
>> nsteps                  = 3000          ; maximum number of steps to
>> integrate
>> implicit_solvent        = GBSA
>> gb_algorithm            = Still
>> nstgbradii              = 1
>> gb_epsilon_solvent      = 80
>> gb_saltconc             = 0
>> sa_algorithm            = Ace-approximation
>> sa_surface_tension      = -1
>> pbc                     = no
>> rgbradii                = 0
>> ns_type                 = simple        ; method of updating neighbor
>> list
>> nstlist                 = 0
>> rlist                   = 0             ; this means all-vs-all (no
>> cut-off)
>> coulombtype             = cut-off
>> rcoulomb                = 0             ; [nm] distance for Coulomb
>> cut-off
>> vdwtype                 = cut-off       ; twin-range cut-off with rlist
>> where rvdw >= rlist
>> rvdw                    = 0             ; [nm] distance for LJ cut-off
>> nstenergy               = 100
>> emtol                   = 5.0
>> emstep                  = 0.01
>> comm-grps               = Protein
>> optimize_fft            = yes
>>
>> Thank you in advance for any comments and suggestions.
>>
>
> If you're using infinite cutoffs, the only acceptable value for rlist is
> 0.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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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