[gmx-users] mdp file to calculate local pressure

[anirban polley]

Dear Justin,
     I am using gromacs-localp of version 4.0.2. for the calculation of
local pressure. But I could not understand what I should put in the mdp
file. Because when I tried by the following below mdp file, it does not even
create tpr file. I have tried by different options as for example by using
Wall but failed to get local pressure profile. I thought that I have write
some thing so that it can be ok for giving local pressure. Could you please
correct my mdp file and write what extra term I should write in my mdp file
to get local pressure.
Thank you very much for your kind help.
Anirban

    title                =  lipid bilayer in water
cpp                  =  /lib/cpp

integrator           =  sd              ; stochastic dynamics -> Langevin!
ld_seed              =  -1              ; random seed for sd
dt                   =  0.002           ; ps !
nsteps               =  250000          ; total 500 ps
nstcomm              =  1               ; freq. for cm-motion removal
tinit                =  0               ; starting time (ps)

constraints          =  all-bonds       ; constraint for all bond lengths
constraint_algorithm =  lincs           ; default
lincs_order          =  4               ; default

nstxout              =  5000            ; T(x_out) 10 ps
nstvout              =  5000            ; T(v_out) 10 ps
nstfout              =  0               ; T(f_out)
nstlog               =  250             ; energies to log (0.5 ps)
nstenergy            =  250             ; energies to energy file

ns_type              =  grid            ; nl type
nstlist              =  10              ; Freq. to update neighbour list
rlist                =  1.0             ; nm (cutoff for short-range nl)

coulombtype          =  Reaction-Field  ; Coulomb interactions
rcoulomb             =  2.0             ; nm (Coulomb cut-off!!)
epsilon_r            =  80.0            ; dielectric constant for reaction
field
vdwtype              =  Cut-off         ; Wan der Waals interactions
rvdw                 =  1.0             ; nm (LJ cut-off)
optimize_fft         =  yes

; Temperature coupling
Tcoupl               =  no              ; no effect when integrator = sd
tc-grps              =  POPC  SM    CHOL  SOL
tau_t                =  0.1   0.1   0.1   0.1
ref_t                =  296   296   296   296

; Pressure coupling
;Pcoupl = no
Pcoupl               =  berendsen
Pcoupltype           =  semiisotropic
tau_p                =  1.0    1.0       ; ps
compressibility      =  4.5e-5 4.5e-5    ; 1/bar (water: 1 atm, 300 K)
ref_p                =  1.0    1.0       ; bar

; Generate velocites in the beginning
gen_vel              =  yes
gen_temp             =  296.0
gen_seed             =  173529
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