[gmx-users] rlist for implicit water

[Justin Lemkul]

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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