[gmx-users] LINCS Constraints - all-bonds or h-bonds?

Michael Shirts mrshirts at gmail.com
Thu Aug 15 21:58:40 CEST 2013

I don't go beyond 2 fs with either all- bonds or h-bonds. Things like kinetic energy start being subtly off.

H-bonds has less chance of failing with large numbers of constraints- less iteration required, especially if bond system cross parallelization boundaries.

If your molecules are < 10 atoms, it probably doesn't matter either way.

Sent from my iPhone

On Aug 15, 2013, at 9:11, "Barnett, James W." <jbarnet4 at tulane.edu> wrote:

> Searching through this mailing list it seems like some have stated that 
> with a 2 fs timestep (dt=0.002), constraints=h-bonds is fine in general.
> The questions I have are:
> 1) What are some personal opinions on when it is ok to switch to h-bonds 
>   from all-bonds for LINCS constraints? Is 2 fs and h-bonds a general 
> practice?
> 2) Also, if typically 2 fs and h-bonds are ok, what time-step do users 
>   (or you personally) generally go to with all-bonds? 
> I am speaking generally here of course. Thanks for your responses.
> -- 
> Wes Barnett | jbarnet4 at tulane.edu
> -- 
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