Re: rigid body simulation with NAMD

From: Victor Kwan (
Date: Thu Nov 28 2019 - 15:53:27 CST

Have you considered QM/MM?

Don't think NAMD have support for rigid bodies.

On Thu, Nov 28, 2019 at 4:17 PM Jovan Dragelj <<>> wrote:

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 protocols).

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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