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

[learnmd]

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 




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