hello,
Hello,
The separation of two strands of DNA is because of PBC. If you consider a very, very, very big box, it is computationally expensive, and you will not see any separation. You can follow my previous discussion for the correction of two separate DNA strands. Putting them in an ITP is useful when you want to apply a restraint to DNA, which must be in one ITP. Furthermore, if there is a covalent bond between DNA and protein, you must merge the ITP.