[gmx-users] rlist for implicit water

[Urszula Uciechowska]

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.

Best regards
Urszula Uciechowska


-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/