Hi Steve and Axel

@Steve:

This is what my initial (for the restart) thermodynamic output shows:

First for original run, at timestep 5000000

Step CPU Press Temp PotEng KinEng TotEng Enthalpy E_vdwl E_hbond n_hbond

E_coul E_pair E_bond E_angle E_dihed E_impro E_mol E_long Volume

5000000 0 530.77605 338.66649 -21386.939 13285.026

-8101.9122 -6970.1244 7432.3133 -28.546358 75

25905.026 -37130.17 6608.0543 4723.902 3575.6798 835.59555

15743.232 -70467.51 146210.24

Now, following for For run restarted at timestep 5000000:

Step CPU Press Temp PotEng KinEng TotEng Enthalpy E_vdwl E_hbond n_hbond

E_coul E_pair E_bond E_angle E_dihed E_impro E_mol E_long Volume

5000000 0 522.60194 338 -21386.939 13258.882

-8128.057 -7013.6991 7432.3133 -28.546358 75

25905.026 -37130.17 6608.0543 4723.902 3575.6798 835.59555

15743.232 -70467.51 146210.24

See, some of the values such as pressure (column 3), Kinetic energy (column

6), Total Energy (column 7), Enthalpy (column 8) are different, but I am not

sure if they are significantly different.

yes. they are. you must be resetting your temperature in some way,

which is the same as giving your system a kick. please check your

input. these data should be identical.

Also, could you explain more what do you mean by nature of MD causing

original and restarted runs to diverge? other than roundoff effects, I

suppose it includes convergence issues, but what else it may include?

it is not really roundoff, it is a truncation that happens when

you, e.g., add or subtract two numbers of different magnitude.

floating point math doesn't commute, so the result of sums

will depend on the order. a restart causes a neighbor list rebuild

and that will change the order in which properties like forces are

summed up which will make the trajectories diverge exponentially.

this is fundamental MD knowledge, check out in, e.g., the allen

and tildesley book.

unless you do fixed point math this will always happen. but this

is a small change and will manifest over time.

the convergence issue is independent. as the slide i was pointing

you to, you may think you have a converged result (the slide is

showing the first derivative(!) not the MSD, those look straight),

but you don't cover all modes in your system. a lot of mistakes

in MD analysis and thus differences in the published literature

happen because people don't know their time scales.

...and it is very difficult (i.e. would take a huge effort) to prove otherwise.

axel.