[gmx-users] Regarding Umbrella sampling

[Amir Zeb]

Hello gmx users,

I want to calculate binding energy for a protein-ligand complex. Obviously,
this is the very first time, I'm handling umbrella sampling, so I faced the
following error.

WARNING 2 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_ncoords' in parameter file



WARNING 3 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_group1_name' in parameter file



WARNING 4 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_group2_name' in parameter file



WARNING 5 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_coord1_type' in parameter file



WARNING 6 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_coord1_geometry' in parameter file



WARNING 7 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_coord1_groups' in parameter file



WARNING 8 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_coord1_dim' in parameter file



WARNING 9 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_coord1_rate' in parameter file



WARNING 10 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_coord1_k' in parameter file



WARNING 11 [file pull.mdp, line 65]:
  Unknown left-hand 'pull_coord1_start' in parameter file



There was 1 note

There were 11 warnings


*The pull.mdp file is this one:*

title       = Umbrella pulling simulation
define      = -DPOSRES_NAD
; Run parameters
integrator  = md
dt          = 0.002
tinit       = 0
nsteps      = 250000    ; 500 ps
nstcomm     = 10
; 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   NAD
tau_t       = 0.5       0.5
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
refcoord_scaling = com
; 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                    = yes
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = NAD
pull_group2_name        = Protein
pull_coord1_type        = umbrella      ; harmonic biasing force
pull_coord1_geometry    = distance      ; simple distance increase
pull_coord1_groups      = 1 2
pull_coord1_dim         = N N Y
pull_coord1_rate        = 0.01          ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
pull_coord1_start       = yes           ; define initial COM distance > 0


Please let me know where I'm making the mistake.

Regards!

-Amir