[gmx-users] What's the practical effect of 'continuation = yes/no'?

Trayder Thomas trayder.thomas at monash.edu
Tue Sep 22 08:21:31 CEST 2015

What exactly does 'continuation = yes' do?

My understanding thus far is that it will move particles in the first step
(using the input velocities) before applying the constraints (LINCS bond
lengths etc.). When continuing a simulation with 'continuation=no' you
would apply constraints twice in a row.

So when using pull code, 'continuation=no' would give you a double-pull,
which would be bad.

But if you were dealing with, for example, only LINCS/SHAKE constraints,
would 'continuation=no' make a practical difference?
The manual states "The relative constraint deviation [for LINCS after one
iteration] will be less than 0.0001 for every constraint". Which suggests
to me that the error in applying a second constraint step would be less
than continuing from a .gro file.

Is my understanding correct?


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