rigid body simulation with NAMD

From: Jovan Dragelj (jovandragelj_at_gmail.com)
Date: Thu Nov 28 2019 - 15:16:38 CST


I have problems finding a proper way to simulate rigid body with NAMD. The
system is an enzyme with a metal cluster for which we do not have FF
parameters and want it treated as a rigid body. Protein needs to be able to
rotate fully, therefore *fixing *atoms won't help.
Unfortunately, I could not make any simulation stable (let's assume other
simulation conditions are fine, since we using relatively standard

1. I tried using *freeEnergy *feature with urestraint, by defining ref
values from the crystal structure and high(er) constants, bond 500, angles
100, barrier for dihedrals 1.0
2. If using *extraBonds *feature, how is this approach any different than
number 1.? I tried this with same values as in 1.
3. I have not tested this but, can this be achieved by using simply high
*constraints* on atoms? Note: We do not have any FF parameters apart from
partial charges.

Details: CHARMM36 FF, NAMD 2.13

Any help would be highly appreciated.

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