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I 2 chains in my system (A and B) I have performed 200 ns MD simulation on it. Now I want to keep chain B static in the trajectory to analyze the interaction between chain A and Chain B. How can I do this? I am getting suggestions where I have been asked to create a position restrain file and then perform MD but I am looking for another solution as I do not want to run MD again.
What do you mean by “analyze the interaction”, calculate contacts, h-bonds, interaction energy? Why do you need one chain to be static for that? There’s nothing in most interaction analyses that would require a static structure of a binding partner, quite the opposite.
I want to analyze the H-bond. but the chain 2 is not a complete protein rather a small peptide and I want to understand the changes happening in the Chain A.
And so what prevents you from doing the h-bond analysis as it is? Does chain B dissociate, misfold, are there PBC issues?
There are no as such issues. But I want to focus solely on the changes in Chain A keeping chain B static and to compare them with the Chain A interactions with another peptide.
Then again, why should chain B be static? Technically you can always restrain it but the dynamics is usually part of the actual research question, so not sure why you’d want to remove it.
you are right dynamics is part of question but I want to answer another question that is what are the changes in protein A in Apo state vs in presence of another peptide. after answering this question I will look into the dynamics and interactions of ProteinA and ProteinB
If the peptide remains bound to chain A, it still meets your requirements. One sensible reason for restraining chain B would be exactly if it dissociated during the simulation, assuming there’s a good scientific reason to study a fictitious interaction, or if you wanted to single out the properties of different conformations of the bound peptide.