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 -- View this message in context: http://gromacs.5086.n6.nabble.com/Water-models-and-diffusion-coefficient-tp5005377p5005409.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists