[gmx-users] deformation of a bilayer

[zozo]

Hi 

I have built a bilayer with different lipids and now I want to apply a deformation (strain) along the x axis of the box using the deform option . but when I give the grompp , it gives me a fatal error for different reasons everytime I change something in the mdp  file . I dont know much about non-equilibration md. my mdp file looks like this: 
When I give acceleration, it says Invalid Acceleration input: 2 groups and 2 acc. values


;define                   = -DFLEXIBLE
integrator               = md
dt                       = 0.03  
nsteps                   = 600000
nstcomm                  = 100
comm-grps         = 


; OUTPUT CONTROL OPTIONS = 
; Output frequency for coords (x), velocities (v) and forces (f) = 

nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 1000  ; Output frequency for energies to log file 
nstenergy                = 100   ; Output frequency for energies to energy file
nstxtcout                = 1000  ; Output frequency for .xtc file
xtc_precision            = 100
xtc-grps                 = 
energygrps               = Lipids Solvent


nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.4

coulombtype              = Shift  ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
epsilon_r                = 15    ; 2.5 (with polarizable water)
vdw_type                 = Shift  ;cutoff (for use with Verlet-pairlist)   
rvdw_switch              = 0.9
rvdw                     = 1.2    ;1.1 (for use with Verlet-pairlist)


;Non-equilibrium MD stuff
acc-grps                 = Lipids Solvent
 accelerate               =  0.1 0.1
;freezegrps               =
;freezedim                =
;cos-acceleration         = 
deform                   = 0.005 0 0 0 0 0

constraints              = none 
constraint_algorithm     = Lincs
continuation             = no
lincs_order              = 4
lincs_warnangle          = 30


Thanks