[gmx-users] LJ parameters in reduced unit

Nicholas Agung Kurniawan nicholas at nus.edu.sg
Fri May 14 10:11:23 CEST 2010

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.





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