[gmx-users] PMF curve in umbrella sampling

[Mana Ib]

Dear Users,

I am doing an umbrella sampling for a protein-ligand complex, wherein I
first did an SMD run for 500 ps and generated 500 configurations, the COM
distances for these configurations start at 1.25nm for conf0 and so on till
6.4nm for conf500. Hence I used a 0.05nm spacing to select configurations
for the umbrella sampling windows.
I have currently completed running 2 windows, each window was subjected to
a 5ns  mdrun.

This is my mdp file parameters

title       = Umbrella pulling simulation
define      = -DPOSRES
; Run parameters
integrator  = md
dt          = 0.002
tinit       = 0
nsteps      = 2500000   ; 5 ns
nstcomm     = 10
; Output parameters
nstxout     = 50000     ; every 100 ps
nstvout     = 50000
nstfout     = 5000
nstxtcout   = 5000      ; every 10 ps
nstenergy   = 5000
; Bond parameters
constraint_algorithm    = lincs
constraints             = all-bonds
continuation            = yes
; 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       = 0.5       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            = umbrella
pull_geometry   = distance
pull_dim        = Y N N
pull_start      = yes
pull_ngroups    = 1
pull_group0     = Chain_A
pull_group1     = NL
pull_init1      = 0
pull_rate1      = 0.0
pull_k1         = 500      ; kJ mol^-1 nm^-2
pull_nstxout    = 1000      ; every 2 ps
pull_nstfout    = 1000      ; every 2 ps


When I use g_wham to plot the histogram and PMF curve for these 2 windows,
my plots don't seem to follow the general trend as given in
tutorials..(figure links below). Is this discrepancy because I have used
only files from 2 windows to plot these? Or are these due to some other
errors in the protocol?

http://i46.photobucket.com/albums/f121/fullmeasure29/histo_2win_zpsff19fe60.png

http://i46.photobucket.com/albums/f121/fullmeasure29/pmf_2win_zps04adb8f7.png