[gmx-users] Re: Water models and diffusion coefficient
Dr. Vitaly Chaban
vvchaban at gmail.com
Mon Feb 11 12:34:16 CET 2013
> 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
> 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)
> 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
> 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,
> ; 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
-- 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
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