[gmx-users] Re: Charge groups II

[Pedro Alexandre de Araujo Gomes Lapido Loureiro]

> Still you give no details...

> Do you treat the whole head group as one charge group?

No. I am using both the charges/charge groups from Chiu (Biophys. J. 69, 1230,
1995).

> Try treating the Choline part as one and the Phosphate part as another.
> And take care  with your Lennard Jones cut-off. Short LJ cut-off with
> large charge groups gives problems too.

Yes, but I am using a 1.8 nm cut-off for this reason. 
My parameters in the mdp file are: 

; OPTIONS FOR ELECTROSTATICS A ND VDW = 
; Method for doing electrostatics = 
coulombtype              = PME
rcoulomb-switch          = 1.0
rcoulomb                 = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field = 
epsilon-r                = 1
; Method for doing Van der Waals = 
vdw-type                 = Shift
; cut-off lengths        = 
rvdw-switch              = 1.6
rvdw                     = 1.8
; Apply long range dispersion corrections for Energy and Pressure = 
DispCorr                 = EnerPres
; Spacing for the PME/PPPM FFT grid = 
fourierspacing           = 0.1
; 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
epsilon_surface          = 0
optimize_fft             = no



Regards, Pedro.

--
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
UFRJ
Brasil