[gmx-users] Re: Charge groups II
Pedro Alexandre de Araujo Gomes Lapido Loureiro
paloureiro at biof.ufrj.br
Fri May 17 14:52:05 CEST 2002
> 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,
> 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
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
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