[gmx-users] shake for water

Berk Hess gmx3 at hotmail.com
Thu Feb 5 21:58:24 CET 2009


Another question, just to be sure.
Have you actually checked that the other code really gets the distances
right up to 1e-12?


> Date: Thu, 5 Feb 2009 12:03:21 -0600
> From: dmobley at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] shake for water
> All,
> A quick question on constraints... I'm using TIP4P-Ew in gromacs 3.3.2
> and am concerned with reproducing energies from another code very
> precisely for several specific snapshots. I am doing a zero-step mdrun
> of a setup with one small molecule and two tip4p-ew water molecules.
> Anyway, I have set the shake tolerance to 1e-12 in the mdp file, but
> to my surprise the internal water distances are good only to 1e-06 and
> 1e-07. Is this expected behavior? Note that I am running in double
> precision. I assumed that, er, the distances should converge to the
> shake tolerance.
> Thanks,
> David
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