[gmx-users] Re: Umbrella Sampling _ pulled ion

[Thomas Schlesier]

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-request at 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 ?