[gmx-users] generating a top file

Shahrokh Safarian safarian at ibb.ut.ac.ir
Sun Jun 10 13:28:20 CEST 2007

Dear colleagues

As you know if we want to introduce a new molecule into Gromacs, the
related parameters for that molecule (e.g. [atoms], [bonds], [pairs],
[dihedrals] and so on) should be inserted to the Gromacs rtp file. In
the Gromacs user's manual (page 100) an example for these types of
topology parameters is propounded for urea molecule. The main question
is how can we obtain these topology parameters for a desired molecule?



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