Steven Neumann wrote:
Dear Justin and Gmx Users,
I run a pulling of my ligand away from my protein with the same mdp file
and I obtained two different plots - Force vs time (The breaking point
occured at different times with different force). Can you please explain?
If you change the stiffness of the spring, you change the magnitude of the
applied force. Thus, the behavior you see will occur either faster or slower,
depending on the strength of the spring.
-Justin
My mdp file:
title = Umbrella pulling simulation
define = -DPOSRES_L
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 250000 ; 0.5ns
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 = 0.9
rcoulomb = 0.9
rvdw = 0.9
; 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
; 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
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 ; simple distance increase
pull_dim = N N Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = Protein
pull_group1 = LIG182
pull_rate1 = 0.016 ; 0.008 nm per ps = 8 nm per ns
pull_k1 = 200 ; kJ mol^-1 nm^-2
--
========================================
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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