[gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

[Johnny Lu]

how long were those simulations?
Were there enough time for the new ensemble to equilibrate, if you changed
ensemble from NVE to NVT?

On Sun, Oct 19, 2014 at 11:34 AM, Wade <wadelv at foxmail.com> wrote:

> Dear Mark and Lu,
>   Thank you very much for your responses.
> Based on your suggestions, I performed some tests:
> 1) I considered the influence of the time-step (with LINCS constraint),
> thermostat, and simulation precision in NVT simulation
> (tip4p water box, 300K, after 2ns NVE simulation).
> Below are results:
> -----------
> Time-step (fs)          thermostat (V or N)      precision (S or D)
>  drift/ns = delt E/av E*100%
> 0.1             V               D               0.3
> 1               V               D               2
> 2               V               D               5.8
>
>
> 0.1             V               S               80
> 1               V               S               1.5
> 2               V               S               6.4
>
>
> 0.1             N               D               0.3
> 1               N               D               2.5
> 2               N               D               20
>
>
> 0.1             N               S               76
> 1               N               S               1.7
> 2               N               S               11.5
> ------------------
> Above results shown that no matter the v-rescale or nose-hoover
> thermostat, the conserved Energy has nearly no drift (~0.3%/ns)
>  when an very small time-step (0.1 fs) has been employed. But, even with
> 0.1fs step length, the integration can only be conserved in
> the double precision simulations.
> For a commonly used time-step, such as 2 fs (with LINCS constraint), the
> drifts of the conserved energy are about 6-7% per ns.
> Such a drift might be not very significant in a short simulation. But, its
> accumulation in a long-time (e.g. several ns) simulation should be huge.
>
>
> 2) I checked the time-dependency of auxiliary dynamics purely, and found
> that it was the origination of the constant-rate drift of conserved energy.
> I also noticed that the exact solution of Eq.7 in bussi’s paper (Eq. A7)
> has been realized in gromacs to get the rescaling factor.
> But, I don’t know what the origination of the integration error is, and
> How can we deal with it.
> As Lu said, does it comes from the summation of dK? If yes, how can we
> deal with the drift when we use an affordable time-step in a long-time
> simulation?
>
>
> With best wishes,
>
>
> Wade
> ‍
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