[gmx-users] Re: Water models and diffusion coefficient

[Dr. Vitaly Chaban]

> Thanks for all your answers. I tried collecting data more frequently (100
> fs), used -trestart as the entire trajectory; however my diffusion
> coefficient for D2O is still in the range 1.4 - 1.5 e-5 cm^2/s.
> Surprisingly, the number of Hbonds, potential energy, density are all what
> would be expected for D2O at 300 K. This is mdrun followed by 1ns each of
> NVT and NPT equilibration.
>
> The way I made the D2O model is by overwriting the mass and charge of HW and
> OW in atomtypes.atp and the itp files for the model. I also updated this
> information in the aminoacids.rtp file.
>
> As a last ditch attempt, I am posting the mdp parameter file that I used for
> the MD run. I greatly appreciate all of your ideas and help. If there is
> anything that comes to mind, which could be the problem, please let me know.
> Thanks again.
>
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 5000000       ; 2 fs * 5000000 = 10000000 fs = 10 ns
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 50            ; save coordinates every 100 fs
> nstvout         = 50            ; save velocities every 100 fs
> nstxtcout       = 50            ; xtc compressed trajectory output every 100
> fs
> nstenergy       = 50            ; save energies every 100 fs
> nstlog          = 50            ; update log file every 100 fs
> ; Bond parameters
> continuation    = yes           ; Restarting after NPT
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-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           = 1.0           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = V-rescale     ; modified Berendsen thermostat
> tc-grps         = System        ; only one component in the system
> tau_t           = 0.1           ; time constant, in ps
> ref_t           = 300           ; reference temperature, one for each group,
> in K
> ; Pressure coupling is on
> pcoupl          = Parrinello-Rahman     ; Pressure coupling on in 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 = 4.76e-5       ; isothermal compressibility of heavy 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            ; Velocity generation is off


A few hints:

-- some water models use the CUTOFF treatment of electrostatics, while
you are using PME. Is PME what you want?

-- The real-space cutoff for the SPC water is 0.9nm, while you are
using 1.0nm. Is it equal to one in your original model, which you are
modifying?

-- You are simulating all-bonds-constrained water. Is it what you need?

-- If you substitute heavy hydrogens with light ones, will the
diffusion constant increase up to 2+ (*10^(-9)) m2/s ?

-- Try to use g_velacc and Green-Kubo formula to compute diffusion. Is
there any difference?

-- Try to specify "-mol" to compute diffusion of the center-of-water,
rather than an average one for all three sites.


-- 
Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark