[gmx-users] Wrong Shake Tolerance

Berk Hess gmx3 at hotmail.com
Mon Mar 16 16:37:49 CET 2009


That will depend on what kind of properties you are looking at and how accurate you want them.
Have inaccurate constraining will usually lead to energy leaking out of your system.
If you use reaction-field this will add energy into the system, probably even more than
the constraints leak, so in that sense the error is probably not significant.

Have a look at your temperature, the constraint inaccuracy should cause a lowering
of the temperature, the steady temperature value will also be affected by your coupling time.


> Date: Mon, 16 Mar 2009 15:55:05 +0100
> From: andreas.frank at ch.tum.de
> To: gmx-users at gromacs.org; Oliver.Demmer at ch.tum.de
> CC: 
> Subject: [gmx-users] Wrong Shake Tolerance
> Dear Gromacs-Users,
> we have the following problem: after running several hundred nanoseconds 
> of a peptide (Gromos FF 53a6) in spc-water (NpT ensemble), we recognized 
> that the tolerance of shake (all-bonds were constrained) was wrongly 
> adjusted: instead of calculating with shake_tol = 0.0001, the value was 
> 0.01. Our question is now if the additional noise we produced in this 
> way makes a repetition of the runs necessary or not? Density, pressure, 
> etc. of the boxes are ok, but we are not sure what kind of artifacts 
> could have arisen due to this wrong setup. The integration time step was 
> 2 fs.
> Thanks for your help and suggestions!
> Cheers,
> Andreas
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