Can I make withdrawals or deposits to my account if I'm using BrokerTransmit to manage my strategy?

Sure, not a problem. The consideration for managing a C2 trading strategy, whether you use Broker Transmit or any other method is really the same. That is, does my C2 model account have the margin and buying power necessary for the trade I'm entering. Your live account could have $10,000 USD or 1,000,000 EUR and the only check we do is, can the model portfolio accept the trade based on the instrument traded and the quantity.

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