[gmx-users] Implicit solvent MD is not fast and not accurate.

[xiao]

Dear Gromacs users:
I did a protein MD using implicit solvent and Amber 99SB force filed. However, i found that the implicit solvent is not faster than explicit solvent, and what is worse is that it is also not accurate.
The system is a protein-ligand complex. Firstly, i run a minimization, and then i did a production MD. The explicit solvent MD can give nearly same strucuture as the crystal structure after 10ns MD. However, there is a
significant change in the ligand after 1ns MD in implicit solvent.
My .mdp file is as follows:
title  = OPLS Lysozyme MD
; Run parameters
integrator = md  ; leap-frog integrator
nsteps  = 10000000 ; 2 * 500000 = 1000 ps, 1 ns
dt  = 0.002  ; 2 fs
; Output control
nstxout  = 1000  ; save coordinates every 2 ps
nstvout  = 1000  ; save velocities every 2 ps
nstxtcout = 1000  ; xtc compressed trajectory output every 2 ps
nstenergy = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
; Bond parameters
continuation = yes  ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1  ; accuracy of LINCS
lincs_order = 4  ; also related to accuracy
; Neighborsearching
ns_type  = grid  ; search neighboring grid cells
nstlist  = 5  ; 10 fs
rlist  = 0  ; short-range neighborlist cutoff (in nm)
rcoulomb = 0  ; short-range electrostatic cutoff (in nm)
rvdw  = 0  ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = cut-off ; Particle Mesh Ewald for long-range
vdwtype         = cut-off
pme_order = 4  ; cubic interpolation
fourierspacing = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps  = system  ; two coupling groups - more accurate
tau_t  = 0.1    ; time constant, in ps
ref_t  = 300   ; reference temperature, one for each group, in K
;
;
comm-mode           =  angular
comm-grps           =  system
;
;
pcoupl  = no ; Pressure coupling on in NPT
pbc      = no  ; 3-D PBC
gen_vel             =  yes
gen_temp            =  300
gen_seed            =  -1
;
;
implicit_solvent    =  GBSA
gb_algorithm        =  OBC ; HCT ; OBC
nstgbradii          =  1
rgbradii            =  0   ; [nm] Cut-off for the calculation of the
Born radii. Currently must be equal to rlist
gb_epsilon_solvent  =  80    ; Dielectric constant for the implicit solvent
; gb_saltconc       =  0     ; Salt concentration for implicit solvent
models, currently not used
sa_algorithm        =  Ace-approximation
sa_surface_tension  = -1
 
Can anyone give me some suggestions?
BW
Fugui