Think your .mdp-file looks reasonable.
If you are totaly unsure you could determine the PMF of two water
molecules. As a reference one can use the radial distribution function
g(r) and calculate the PMF as
V_pmf(r) = -kT LN(g(r))
One side note:
Since the force constant you are using is relative large you will need a
relative small distance increment between the individual umbrella windows.
Greatings
Thomas
Am 25.07.2013 13:56, schrieb gmx-users-requ...@gromacs.org:
After running for 100 ps, I visualized the pullf_umbrella.xvg, in this plot I
found the F value around 100 kJ/mol/ns. But force constant which I had set in
md_US.mdp file was 4000 KJ/mol/ns. Does this difference show me that the US has
not done properly?
;define??? ??? = -DPOSRES ???
integrator????? = md??????????? ; leap-frog integrator
nsteps????????? =100000???????? ; 1 * 100000 = 100 ps
dt????????????? = 0.001???????? ; 1 fs
nstcomm???? = 10
tinit?????? = 0
; Output control
nstxout???????? = 5000?????????? ; save coordinates every 100 ps
nstvout???????? = 5000?????????? ; save velocities every 100 ps
nstenergy?????? = 1000?????????? ; save energies every 2 ps
nstfout???? = 5000
nstxtcout?? = 5000??? ??? ??? ??? ; every 10 ps
continuation??? = yes??????????? ; first dynamics run
constraint_algorithm = lincs??? ; holonomic constraints
constraints???? = h-bonds???? ; all bonds (even heavy atom-H bonds) constrained
lincs_iter????? = 1???????????? ; accuracy of LINCS
lincs_order???? = 4???????????? ; also related to accuracy
; Neighborsearching
ns_type???????? = grid????????? ; search neighboring grid cells
nstlist???????? = 5???????????? ; 10 fs
rlist?????????? = 1.2?????????? ; short-range neighborlist cutoff (in nm)
rlistlong?????? = 1.4
rcoulomb??????? = 1.2?????????? ; short-range electrostatic cutoff (in nm)
rvdw??????????? = 1.2?????????? ; short-range van der Waals cutoff (in nm)
vdwtype???????? = switch
rvdw_switch???? = 1.0
; 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
ewald_rtol????? = 1e-5
optimize_fft??? = yes
; Temperature coupling is on
tcoupl????????? = Nose-Hoover???? ; modified Berendsen thermostat
tc-grps???????? = Protein_POPC Water_Ces_CL??? ??? ; two coupling groups - more
accurate
tau_t?????????? = 0.5?? 0.5?? ??? ; time constant, in ps
ref_t?????????? = 310?? 310??? ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl????????? = Parrinello-Rahman??????????? ; no pressure coupling in NVT
pcoupltype????? = semiisotropic
tau_p?????????? = 4
ref_p?????????? = 1.01325 1.01325
compressibility = 4.5e-5 4.5e-5
; Periodic boundary conditions
pbc???????????? = xyz?????????? ; 3-D PBC
; Long-range dispersion correction
DispCorr??? = EnerPres
; Pull code
pull??????????? = umbrella
pull_geometry?? = position
pull_dim??????? = N N Y
pull_start????? = yes
pull_ngroups??? = 1
pull_group0???? = POPC
pull_group1???? = Ces_ion
pull_init1????? = 0.0 0.0 0.0
pull_rate1????? = 0.0 0.0 0.00
pull_vec1??? = 0 0 1
pull_k1???????? = 4000????? ; kJ mol^-1 nm^-2
pull_nstxout??? = 1000????? ; every 2 ps
pull_nstfout??? = 1000????? ; every 2 ps
; Velocity generation
gen_vel???????? = no?????????? ; assign velocities from Maxwell distribution
refcoord_scaling??? = com
Would you please let me know your suggestions ?
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