Please I am a beginner in GROMACS simulation and happens to be doing my undergraduate final year project on molecular dynamics simulation. I am working on the use of the martini model in simulation for coarse grain sugar. I have to modify the bondfree.c file to supply coordinates of the atoms, mixing parameter, and boltzmann constant as initial values to my starting method which also process it to find the potential. I also, amongst the initial values, have to get the values for an euclidian distance in order to find theta for the calculation as per the algorithm I'm using.... I am having serious difficulty, can anyone help me please.......
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