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Margining & Liquidations: Multi-Collateral
Collateral Currency
Multi-collateral linear contracts use the USD value of the available collateral currencies adjusted using value haircuts. Haircuts and conversion fees apply to non-USD collateral, see:
For the Multi-Collateral margin account all positions and collateral are dollarised and haircuts are applied to non-USD collateral. Due to the application of haircuts, the Collateral Value differs from the Balance Value when holding non-USD currencies. 
The Margin Equity is the Balance Value multiplied by the dollar rate and with haircuts applied to non-USD currencies, plus unrealised profit or loss as Margin. The formula is displayed below:
Margin Equity = [Balance Value in USD * (1-Haircut)] + (Total Unrealised Profit/Loss as Margin in USD)
See glossary for more details.
Margin Netting
Margin netting only applies when trading perpetual and fixed maturities with the same underlying. Margin netting only occurs between cross margined long and short positions in the same wallet, meaning that if one or both of the legs are using isolated margin it will not apply. 
For instance, there is margin netting between a cross margined long BTC/USD Perp position and a cross margined short BTC/USD fixed maturity position.
The Total Margin Requirement will then be calculated as:
Total Margin Requirement = Max(Margin Long Positions, Margin Short Positions)
This means that the margin requirement of only long or short positions is counted, whichever is greater. This applies to all margin parameters (i.e. Initial Margin and Maintenance Margin).
Margin netting allows traders to efficiently exploit price differences across maturities. For instance, if you think that the price of Futures A is too high compared to Futures B, you could open a short position in A and a long position in B. This will turn a profit if the difference decreases. Margin netting ensures that margin requirements for this position are not excessive.
Cross vs Isolated Margin
When trading Multi-Collateral (MC) Futures on Kraken traders have the option to choose between isolated and cross margin on a contract level.
See "Setting Leverage" in Trading Multi-Collateral Futures to learn about how to configure Cross or Isolated margin.

Isolated Margin

Isolated margin allows a trader to be in full control on how much leverage they are taking on a position and how much funds they want to have at risk at any given time. The Isolated Margin indicates the Initial Margin the system sets aside for the position opened for the specific contract, which is the Margin allocated to a position and the only funds at risk.
Initial Margin set aside for an Isolated position is excluded from Cross Risk margin calculations so Cross Liquidations do not impact Isolated Margin set aside, unless there is an account-wide liquidation then the isolated position will also get liquidated.
Note: Funding rate payments in isolated positions are deducted from the general wallet balance rather than being included in the PnL which can cause liquidation in isolation.

Cross Margin

Cross margin allows a trader to use all the funds available in the margin wallet to collateralise their positions excluding any potential margin set aside on an isolated position. The leverage level for the positions is determined by their size in relation to the collateral value, known as Effective Leverage.
Margin preferences apply per contract and can only be changed before opening a position. Once a position is open its margin preferences cannot be changed. To make changes to the margin preferences, the open position in that contract must first be closed. 
The system allows opening of both isolated and cross positions concurrently but not on the same contract. For example, you can open an isolated position on BTC/USD and a cross position on ETH/USD, but it is not possible to open both an isolated and cross position on BTC/USD. 
Note that unrealised profits on Isolated positions cannot be used to margin cross positions and vice versa. 
→ Isolated position gets liquidated.