grompp warns about md + FEP even for fully coupled states
gmx grompp with FEP .mdp inputs and non-SD integrators issues
WARNING 1 [file grompp.mdp, line 62]: For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used
It does so even for a fully coupled state. We should not be issuing warnings when there's no data to support that, because that will train users to use -maxwarn.We should check if this warning is still appropriate
- at least check the git history for which Redmine added it - is full VDW but no charge OK?
- is the warning based on ancient implementations and needs updating?
If we keep it, it should be sensitive to the calculation being done. For example, even slow growth (TI) starting from a not-nearly decoupled state should not issue it. FEP should only issue it for suitable values of lambda (if any).
Change grompp decoupling SD warning to note
The warning that grompp issues when decoupling a molecule
without the use of the SD integrator has been changed to a note,
since there are valid use cases for using normal MD when not
running in the completely decoupled state.
Note that checking for actual decoupled VdW states requires a lot of
code and would still not be 100% correct.
#2 Updated by Berk Hess about 1 year ago
The user can manually modify the topology to decouple a molecule. Do we want to check for that? Or do we rather want to reduce false positives and accept some false negatives? Then we would only need to check if we have a fully decoupled state, i.e. couple-lam0/1 = none with lambda=0/1.