[gmx-users] Position restraints

[alex rayevsky]

Dear All!
I have a doubt about the rightness of ligand/molecule integration in the
topology file. I'm using an amber (tleap) or swissparam.ch to build a
topology of the residue (modified trna). Is it neccessary to generate a
position restrain file (genrestr program) for this residue or not? I've
started both dynamics with/without posrestraints on my residue, however I'm
really not sure that my results from both of them are different. But I want
to do everything in right way, so what can you say about this?

Thank you

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