[gmx-users] RMSD reproducibility

Biplab Ghosh ghosh.biplab at gmail.com
Mon Feb 15 18:21:46 CET 2016

Dear Gromacs Users,

I have the following question:

Suppose I repeat a simulation, keeping everything exactly the same.
What will happen to RMSD? Will it be exactly same with the previous run?
If not, then how much variation is expected?

To check this, I ran two independent simulations:
1) upto t=100ns using 216 processors and
2) upto t=200ns using 432 processors.
Everything else were kept unchanged!

The calculated RMSD for upto t=100ns was quite different.
Am I doing something  wrong? Please explain.


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