Hi all,
I am trying to perform MD simulations on a system where using reduced units is necessary. The Gromacs manual provides a table (Table 2.4) on how to calculate the reduced units. However, many quantities listed in the table (time, temperature, energy, etc) are related to the SI unit through LJ parameters (sigma and epsilon). The problem is, my system does not accept standard LJ: I need to feed a user-specified table. In this case, how should I calculate the reduced units? Can I just use any two distance and energy values which are characteristic for my system to replace sigma and epsilon, respectively? Many thanks in advance. Regards, Nicholas
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