[gmx-users] using PME option

[Alan Wilter Sousa da Silva]

Hi List!

	From my experience with MD I've never user PME.  So thanks to
GROMACS I had this opportunity now.  I build a system composed of a
protein in a solvent box (water) using at least 1.5 nm of hydration shell
over protein, since I'd planned to use cut-off (both vdW and coulomb) of
1.5 nm.  However I had to include ions to my system and now I decided to
use PME.  As I believe, I don't need to use so large cut-off, is that
right?  My actual mdp file (part) follows as it is:

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or no =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 1.5 ;  (CHANGE?)

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = PME
rcoulomb-switch          = 0      ;   (useless?)
rcoulomb                 = 1.5    ;   (CHANGE? 0.9 is a good value?)
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r                = 1
; Method for doing Van der Waals =  (PME has no effect here, right?)
vdw-type                 = Shift  ;   (how new rlist will affect it?)
; cut-off lengths        =
rvdw-switch              = 1.4    ;   (CHANGE?)
rvdw                     = 1.5    ;   (CHANGE?)
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                 = EnerPres
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters =
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = yes


I would thank very much any help here.  So what changes should I have to
do about rlist, rcoulomb and vdW options and values, if necessary or to
improve performance?

Cheers,

-----------------------
Alan Wilter S. da Silva
-----------------------
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil