[gmx-users] 4-site rigid body model

Sanku M msanku65 at yahoo.com
Fri Nov 19 01:22:50 CET 2010


  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.


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