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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?
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?
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.