[gmx-users] Energy drift

[Mark Abraham]

On Wed, Aug 20, 2014 at 3:55 PM, Xiaobin Cao <xcao at lsu.edu> wrote:

> Thanks for your response, Mark. Can you help me to check the parameters
> for my mdp file to see if it is correct? Can you send me a mdp file for
> NVE? I will test it today.
>

Just turn off T and P coupling!


> By the way, my GROMACS version is single precision? Does it matter?


Generally not, if everything else is correct. But you can try double
precision to see for yourself.

Mark


> >Given that their bond constant for N-N is ~4.5 times higher than their
> bond
> >constant for C-H, and both have comparable equilibrium lengths, and
> >unconstrained C-H bonds are normally treated with either 1fs or 0.5fs, and
> >that time step should be rather shorter than the period of bond
> >oscillation, I'd have serious reservations about the quality of that
> model,
> >and your results suggest reason for that. If you've got the parameters
> >right, then you should be able to suppress (post-equilibration) NVE drift
> >from integration inaccuracy by taking a time step that is small enough.
> How
> >small is small enough?
>
> >Mark
>
> >Thank you
>
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