Hi,
I have a molecule consisting of 4 sites which have fixed relative positions
interacting only through LJ and coulomb interaction. I was wondering how can I
do MD simulation in GROMACS keeping the geometry unchanged . Is just putting
constraints along all the possible distances and using LINCS good enough for
maintaining the geometry ? Or , Does one need to also make sure the angles are
also unchanged but I am not sure how to do that ? I was wondering what will be
an optimum ways of dealing with such a 4-site system. I guess, Settle can not
be used for such a 4-site system.
Thanks
Sanku
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