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Dear Gromacs Community,
The system we are simulating has 8 protein chains, DNA, and RNA
we would like to simulate the dsDNA separation followed by the RNA-DNA hybridization. we need to use an accelerated sampling method, so we decided to use the AWH!
I have a problem with the AWH parameters and the setup of the pull code.
Since I want to observe the dsDNA separation, should I choose the pull code geomtery=distance?
To describe the base pair opening, Should I choose two pull groups only in the DNA or 10 pull groups since the system is made up of several parts? How can I choose the reaction coordinate in this case?
Thank you so much for your help!
I have a follow up question
We want to observe the melting of 8 base pairs. I chose 8 pull coordinate . Each group is defined by 2 pull coordinate. The RC is the distance between the N1 atom of the purine (base A or G) to the N3 atom of the pyrimidine (base T or C) to define the hydrogen bond of the opening base pair. I chose the RC according to the base pair opining tutorial using AWH , the choice of the RC is right? Should I choose only one pull coordinate to observe the opening in the first bp then make a new mdp to observe the second opening and so on ? or one mdp is enough if I choose the AWH bias to be independent?
Any suggestions are greatly appreciated!
This depends on what you want to do. AWH biases the simulation along one or more reaction coordinates computes the free-energy. If you want to compute the free-energy of the opening of one base pair for 8 different pairs, you need to do 8 separate simulations with each one, different, reaction coordinate. If you want to see 8 base pairs open simultaneously, there might be many different ways to achieve that.