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 f
On 2013-02-09 19:26, learnmd wrote:
For a simulation that is 300 ns long (after NVT and NPT equilibration steps
of 1 ns each), I am saving output every 2 ps. The time step is 2 fs.
nstxout = 1000 ; save coordinates every 2 ps
nstvout = 1000 ; save velocities eve
For a simulation that is 300 ns long (after NVT and NPT equilibration steps
of 1 ns each), I am saving output every 2 ps. The time step is 2 fs.
nstxout = 1000 ; save coordinates every 2 ps
nstvout = 1000 ; save velocities every 2 ps
nstxtcout = 1000
What time period do you use to fit the mean-squared displacement to
determine the diffusion coefficient? g_msd determines the diffusion
coefficient by performing a linear fit over the time interval specified by
the -beginfit and -endfit flags, which default to 10% and 90% of the
simulation time (if
Thanks for your reply David. However, what I am concerned is that with the
parameters, q[O] = -0.870, and q[H] = 0.435, the original author reported
diffusion coefficient very close to 2.0 e-5 cm^2/s. My values for even much
longer simulations (200 ns after 1ns each of NVT and NPT equilibration)
re
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