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Hello all,
I recently ran an umbrella simulation, pulling 2 proteins apart. My PMF curve looks correct but for some reasons, I only see 1 peak on my histogram plot. I have changed wham to bins -50 per another post suggestion but that did not seem to help.
Here is my umbrella sampling mdp file (Im 100% sure my steered MD was good):
title = umbrella sampling md
define = -DPOSRES_RECEPTOR
; Run parameters
integrator = md
nsteps = 1000000 ; 2 ns
dt = 0.002
; Output control
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
continuation = yes
constraint_algorithm = lincs
constraints = all-bonds ; constrain all bonds
lincs_iter = 1
lincs_order = 4
; Neighbor searching and vdW
cutoff-scheme = Verlet
nstlist = 20
vdwtype = Cut-off
vdw-modifier = Potential-shift
DispCorr = EnerPres
rvdw = 1.0
rlist = 1.2
rcoulomb = 1.0
coulombtype = PME
pme_order = 4
fourierspacing = 0.125
; Temperature coupling
tcoupl = v-rescale
tc-grps = Protein Non-Protein ; two coupling groups
tau_t = 1.0 1.0
ref_t = 310 310
; Pressure coupling
pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype = isotropic
tau_p = 5.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; Velocity generation
gen_vel = no
;COM Pulling
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = Protein1
pull_group2_name = Protein2
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N Y N
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.0 ; restrain in place
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
Thanks!