normal Warning oscillational period with Elnedyn

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2 years 11 months ago #9071 by moon
Hi,

I'm running a CG simulations (protein in a bilayer) on GPU using the Elnedyn approach. However i get this warning

"The bond in molecule-type Protein_A between atoms 1 BB and 3 BB has an
estimated oscillational period of 9.7e-02 ps, which is less than 10 times
the time step of 1.0e-02 ps.
Maybe you forgot to change the constraints mdp option."

Reading around in the forum it seems to me that this should be associated with the high force constant on the BB-BB bond and it should be safe to ignore the warning and carefully check my system during the simulation. Is it the right approach or should I change/check something in my topology or mdp file? I'm using the default from CHARMM-GUI. Thanks a lot for your help

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2 years 11 months ago #9073 by xavier
Replied by xavier on topic Warning oscillational period with Elnedyn
Hi,

Indeed this is a classic warning due to the tightness between bond’s vibration (BB-BB) and the time step used. Ideally you want the time step to be small enough to be able to describe the vibration of the bonds bonds … well the warning is reasonable but « users » know about it and the warning can be ignored as we didn’t observe bad further behavior.
But it is always good to be aware of the fact in case things go wrong.
Alternatively you can you can reduce the time step for « équilibration » and return to you original value.

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2 years 10 months ago - 2 years 9 months ago #9102 by SophieKing
Replied by SophieKing on topic Warning oscillational period with Elnedyn

xavier wrote: Hi,
But it is always good to be aware of the fact in case things go wrong.
Alternatively you can you can reduce the time step for « équilibration » and return to you original value.


Thank you, now some things make sense to me...
Last edit: 2 years 9 months ago by SophieKing.

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