Steven Neumann wrote:
Dear Gmx Users, Dear Justin,
I pulled my ligand away from my protein. Ligand was attached to lower
part of my protein, I pulled in Z coordinate it using:
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 5000000 ; 2 * 5000000 = 10 ns
dt = 0.002 ; 2 fs
tinit = 0
nstcomm = 10
; Output control
nstxout = 50000 ; save coordinates every 100 ps
nstvout = 50000 ; save velocities every
nstfout = 5000
nstxtcout = 5000 ; every 10 ps
nstenergy = 5000
; Bond parameters
continuation = yes ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 0.9 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
rvdw = 0.9 ; short-range van der Waals cutoff (in nm)
ewald_rtol = 1e-5 ; relative strenght of the Ewald-shifted potential
rcoulomb
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
optimize_fft = yes
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc_grps = Protein_LIG Water_and_ions ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 298 298 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 1.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; assign velocities from Maxwell distribution
; These options remove COM motion of the system
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = Protein
pull_group1 = LIG182
pull_init1 = 0
pull_rate1 = 0.0
pull_k1 = 200 ; kJ mol^-1 nm^-2
pull_nstxout = 1000 ; every 2 ps
pull_nstfout = 1000 ; every 2 ps
Following Justin's tutorial I used perl script to extract coordinate for
each window.
0 2.4595039
1 2.4745028
...
500 8.74
My ligand at the begining was at such distance as it was in the lower
part of the protein. Then I used 0.1 nm spacing at the begining (till 4
nm) and 0.2 nm later on.
And following equilibration in each window I run umbrella sampling for
10ns in app 49 windows:
Run parameters
integrator = md ; leap-frog integrator
nsteps = 5000000 ; 2 * 5000000 = 10 ns
dt = 0.002 ; 2 fs
tinit = 0
nstcomm = 10
; Output control
nstxout = 50000 ; save coordinates every 100 ps
nstvout = 50000 ; save velocities every
nstfout = 5000
nstxtcout = 5000 ; every 10 ps
nstenergy = 5000
; Bond parameters
continuation = yes ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 0.9 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
rvdw = 0.9 ; short-range van der Waals cutoff (in nm)
ewald_rtol = 1e-5 ; relative strenght of the Ewald-shifted potential
rcoulomb
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
optimize_fft = yes
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc_grps = Protein_LIG Water_and_ions ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 298 298 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 1.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; assign velocities from Maxwell distribution
; These options remove COM motion of the system
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = Protein
pull_group1 = LIG182
pull_init1 = 0
pull_rate1 = 0.0
pull_k1 = 200 ; kJ mol^-1 nm^-2
pull_nstxout = 1000 ; every 2 ps
pull_nstfout = 1000 ; every 2 ps
My PMF profile:
http://speedy.sh/zerqZ/profile.JPG
My histogram: http://speedy.sh/PyhnN/Histo.JPG
Why g_wham takes into account distances below 2.45 nm as the 1st
structure was at 2.45. If I get rid of the distances below 2.45 (those
weird values PMF values) I obtain beautiful profile:
http://speedy.sh/TUXGC/profile1.JPG
Please, explain!
The way you're thinking about distance is not consistent. Again, this is a
hazard of trying to map my tutorial onto your problem. You say you have a
ligand bound to the "lower part" of your protein, and then you're pulling in the
z-direction. The COM distance (as measured by g_dist and extracted using my
script) is not equivalent to the distance along the reaction coordinate, if that
reaction coordinate is only one dimension. In the tutorial, it was. Here, it
is not, hence the massive sampling defects that you're observing and
considerable redundancy in many of your windows.
Check the output of grompp for the actual restraint distances that mdrun will
interpret. They are printed to the screen.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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