[gmx-users] Two atom oscillational period less than the time step

[Alessandra Villa]

Hi,

On Tue, Dec 3, 2019 at 7:37 AM Mijiddorj B <b.mijiddorj at gmail.com> wrote:

> Dear GMX users,
> Hello, I would like to discuss the grompp message that tells the bonded
> atoms oscillational period less than 10 times the time step. I am using
> 0.002 ps time step.


The choice of the time step depends on the force field parameter set.
and bond oscillation of light atoms (e.i H) determines the time step.
I suggest to follow the indication given by the developers of the force
field you are using.

The simulation was stopped because of LINCS warming.
>
>
Pls note that constraints can be applied to a) only bond containing H  b)
to all bonds (but and also to angle and so on).

Best regards
Alessandra


> Is it need to decrease time step at least 10 times?
>
> Instead of this, can I remove constraint and use the 0.0005 ps time step?
>
> On the other hand, after long equilibration with 0.0001 time step, can I
> increase the time step until 0.001?
>
> How can I solve this problem?
> If you have any experience, please let me advice. Thank you.
>
> Regards,
> Mijiddorj
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