[gmx-users] Wrong Shake Tolerance

Andreas Boozo Frank andreas.frank at ch.tum.de
Mon Mar 16 15:55:05 CET 2009

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!



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