Umbrella stage

The umbrella-stage is the stage of an Artemia embryo after it has broken out of the cyst shell but before it is released from the cyst membrane that envelopes the nauplius. It is therefore slightly smaller than the nauplius and immobile. For fish larvae with a critically small mouth opening, it offers the opportunity to offer a smaller live feed particle. In Vietnam, it seems to be common practice in some cobia hatcheries and at least one study demonstrates the possibility to skip the use of rotifers by using umbrella-stage Artemia in cobia (Rachycentron canadum) larviculture (Van Can Nhu et al, 2010). 

As discussed in Section Reweighting, it is sometimes useful to compute free energy as a function of a posteriori chosen CVs different from the biased ones. This is typically done in WTMetaD using a reweighting scheme introduced in Ref. 49. Here the time derivative of the partition function is estimated on the fly and allows consistent combination of data obtained at different stages of the simulation. An alternative has also been recently proposed on the basis of the classical umbrella sampling formula. Both these techniques are specific for WTMetaD. 

In the first step of stage 1, all atoms (5000-25000 atoms for a typical application to an enzyme-catalyzed reaction) are treated on the same footing. In this step, one calculates a one-dimensional potential of mean force (PMF) as a function of the distinguished reaction coordinate 2 by a classical molecular dynamics simulation. Any method for calculating classical mechanical PMFs could be used for example, one can use the CHARMM program to carry out this step by employing molecular dynamics simulation with umbrella sampling. As discussed below, this provides an approximation to the free... 

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