[gmx-users] pulling

[mohsen ramezanpour]

Dear All
I am using this configuration.mdp file for pulling.this is the same as
umbrella sampling,of course I have changed some parts of it
according to my problem(protein-ligand free energy).but when i use grompp
this warning is occuring.
WARNING 1 [file configuration.mdp, line unknown]:
  Unknown left-hand 'continuation' in parameter file

WARNING 2 [file configuration.mdp, line unknown]:
  Unknown left-hand 'pull' in parameter file

WARNING 3 [file configuration.mdp, line unknown]:
  Unknown left-hand 'pull_geometry' in parameter file

WARNING 4 [file configuration.mdp, line unknown]:
  Unknown left-hand 'pull_dim' in parameter file

WARNING 5 [file configuration.mdp, line unknown]:
  Unknown left-hand 'pull_start' in parameter file

WARNING 6 [file configuration.mdp, line unknown]:
  Unknown left-hand 'pull_ngroups' in parameter file

WARNING 7 [file configuration.mdp, line unknown]:
  Unknown left-hand 'pull_group0' in parameter file

WARNING 8 [file configuration.mdp, line unknown]:
  Unknown left-hand 'pull_group1' in parameter file

WARNING 9 [file configuration.mdp, line unknown]:
  Unknown left-hand 'pull_rate1' in parameter file

WARNING 10 [file configuration.mdp, line unknown]:
  Unknown left-hand 'pull_k1' in parameter file

I copy my .mdp file.where of it is wrong??
title        = Umbrella pulling simulation
define        = -DPOSRES
; Run parameters
integrator    = md
dt        = 0.002
tinit        = 0
nsteps        = 250000    ; 500 ps
nstcomm        = 1
; Output parameters
nstxout        = 5000        ; every 10 ps
nstvout        = 5000
nstfout        = 500
nstxtcout    = 500        ; every 1 ps
nstenergy    = 500
; Bond parameters
constraint_algorithm     = lincs
constraints        = all-bonds
continuation         = yes        ; continuing from NPT
; Single-range cutoff scheme
nstlist        = 5
ns_type        = grid
rlist        = 1.4
rcoulomb    = 1.4
rvdw        = 1.4
; PME electrostatics parameters
coulombtype    = PME
fourierspacing  = 0.12
fourier_nx    = 0
fourier_ny     = 0
fourier_nz    = 0
pme_order    = 4
ewald_rtol    = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl         = Nose-Hoover
tc_grps        = Protein Non-Protein
tau_t        = 0.1 0.1
ref_t        = 310 310
; Pressure coupling is on
Pcoupl        =  Parrinello-Rahman
pcoupltype    = isotropic
tau_p        = 1.0
compressibility    = 4.5e-5
ref_p        = 1.0
; Generate velocities is off
gen_vel        = no
; Periodic boundary conditions are on in all directions
pbc        = xyz
; Long-range dispersion correction
DispCorr    = EnerPres
; Pull code
pull        = umbrella
pull_geometry    = distance
pull_dim    = N Y N
pull_start    = yes        ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0    = protein
pull_group1    = LIG
pull_rate1    = 0.01        ; 0.01 nm per ps = 10 nm per ns
pull_k1        = 1000        ; kJ mol^-1 nm^-2

thanks in advance
Mohsen
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